from:"fsbuild"

Re: [Freesurfer] mri_glmfit error: matrix is rank-deficient by 18

2024-10-05 Thread fsbuild

External Email - Use Caution

 I’m not sure it will make a difference, but you could try downloading, 
installing and running one of the current development builds for the Silicon 
Mac.  You could try this download link,
https://secure-web.cisco.com/1knximumtc7HGhko0zDsKDfS2Nqhp3y3blHXGS-mPKcRQ-2luavC6Mq9rvDUJYmUM_VbyhxAAIBhGwI31zlmxUtqwDUNwa4YthPxUvazsca50xAOHgKTqwZiT6-xSv-TigJXP41F06y1wQ2hv5FQINurFhlYJSd3kvnYeiKf3yr-H9mJQgLpuJeTgYsb9w5GRt9VWSpFSYvgj38dbu76zQiUysDyRGMKr9EJ8QN6S2z9adVQ21A7L5-tsy90yaWA3WUmhVR180cvBo6m3TNg0LZFnYHWbh2Fd1YzjuBjEpgQqGOWnytWPYTIbzKjhngHS/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Fpub%2Fdist%2Ffreesurfer%2Fdev%2Fstable%2Ffreesurfer-macOS-darwin_arm64-dev.pkg
- R.

On Oct 4, 2024, at 12:20, Shawn Flanagan 
 
wrote:External Email - Use 
CautionHi FreeSurfer Developers,
I am attempting to compute group analysis as described in the FS tutorial and 
it appears to run but with the following message at the end for each 
contrast:
Writing results
  CON-ACLleft
    maxvox sig=-2.57471  F=9.30914  at  index 155198 0 
0    seed=1728409464
Computing efficiency
/Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4.13.2/itk/4.13.2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx:
 vnl_qr::solve() : matrix is rank-deficient by 18
/Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4.13.2/itk/4.13.2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx:
 vnl_qr::solve() : matrix is rank-deficient by 18
/Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4..13.2/itk/4.13.2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx:
 vnl_qr::solve() : matrix is rank-deficient by 18
/Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4.13.2/itk/4.13.2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx:
 vnl_qr::solve() : matrix is rank-deficient by 18
/Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4.13.2/itk/4.13..2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx:
 vnl_qr::solve() : matrix is rank-deficient by 18
/Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4.13.2/itk/4.13.2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx:
 vnl_qr::solve() : matrix is rank-deficient by 18
/Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4.13.2/itk/4.13.2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx:
 vnl_qr::solve() : matrix is rank-deficient by 18
/Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4.13.2/itk/4.13.2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx:
 vnl_qr::solve() : matrix is rank-deficient by 18
/Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4.13.2/itk/4.13.2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx:
 vnl_qr::solve() : matrix is rank-deficient by 18
/Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4.13.2/itk/4.13.2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx:
 vnl_qr::solve() : matrix is rank-deficient by 18
/Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4.13.2/itk/4.13.2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx:
 vnl_qr::solve() : matrix is rank-deficient by 18
/Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4.13.2/itk/4.13.2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx:
 vnl_qr::solve() : matrix is rank-deficient by 18
/Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4.13.2/itk/4.13.2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx:
 vnl_qr::solve() : matrix is rank-deficient by 18
/Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4.13.2/itk/4.13.2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx:
 vnl_qr::solve() : matrix is rank-deficient by 18
/Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4.13.2/itk/4.13.2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx:
 vnl_qr::solve() : matrix is rank-deficient by 18
/Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4.13.2/itk/4.13.2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx:
 vnl_qr::solve() : matrix is rank-deficient by 18
/Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4.13.2/itk/4.13.2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx:
 vnl_qr::solve() : matrix is rank-deficient by 18
/Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4.13.2/itk/4.13.2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx:
 vnl_qr::solve() : matrix is rank-deficient by 18
  CON-ACLright
    maxvox sig=2.75772

Re: [Freesurfer] Freesurfer stopped working after updating to Ubunto 24.04.1 LTS

2024-10-05 Thread fsbuild

External Email - Use Caution

Hello Raj,
Sometimes when OS’s update to a new major revision, the system libraries change
such that software installed under the old OS version is not backwards
compatible with the new OS version. I think we may have already mentioned
on the list that the current freesurfer builds/releases do not yet support
installing or running on Ubuntu 24. VM applications like Oracle’s
VirtuaBox, and those from VMware, etc., support making a snapshot and/or backup
copy of the VM’s disk image.. So for example, before upgrading from
Ubuntu 22 to Ubuntu 24 you could clone the current VM (as VirtualBox
calls it) so that you have a copy (or a 2nd) VM that is your old Ubuntu 22
system. You just need to have enough disk space to store snapshots
and/or clones/backups of the virtual machine. Sorry I don’t have a
workaround to run 7.4.1 on Ubuntu 24.
- R.

On Oct 5, 2024, at 06:26, Raj Agarbattiwala
wrote:External Email - Use
CautionDear Developers
I installed Freesurfer 7.4.1 when using Ubuntu 22 in an Oracle VM on Windows 10
as a host OS. However, I recently updated to Ubuntu 24.04.1 LTS (I still regret
it), and after that, Freesurfer stopped working. It shows "bash:
/usr/local/freesurfer/7.4.1/ SetUpFreeSurfer.sh: No such file or directory" as
an error message. I tried to re-install Freesurfer, and it showed the following
error message:
The following packages have unmet dependencies: freesurfer : Depends:
libncurses5 but it is not installable Depends: libc6 (< 2.36) but
2.39-0ubuntu8.3 is to be installed E: Unable to correct problems, you have held
broken packages.
I am a Neurosurgeon in Mumbai. I have beginner-level knowledge of programming.
Please help me out.
Regards
Raj Agarbattiwala
Jaslok Hospital and Research Center,
Mumbai___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://secure-web.cisco.com/11xpk6NwlTzyo7_bufXgr7-1Uj_QbwYQSmscCI2OEi7z2itlW3LRgb34evuuks6a3OPrlVztfJH9MVuzopjo-mfkhgUL3YfhvuFnWCsKKFIw3e-i2Ly7v73B23i4MVpWvuitkzYYtD45D2aqPMUs2F_2vgX9ZO-Pq0-TL2PxQBUS4AS-viI7Xyg76nG2WhIYTC5WisRbZOgH_V6r_F2wGXPQKqHg1rhQWLF3v9qkJnwAN5rivcVmijYRuW7a0i6m9L9xoHRK8nwHRHEl9wPV6SUT_Vb_DmZzkgigZTR2qzSDTkJ-Ap84ldIcjWnoWi2cyw0x1hYr_O7a5CaVpWxd5gw/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Mass General Brigham
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline
.
Please note that this e-mail is not secure (encrypted). If you do not wish to
continue communication over unencrypted e-mail, please notify the sender of
this message immediately. Continuing to send or respond to e-mail after
receiving this message means you understand and accept this risk and wish to
continue to communicate over unencrypted e-mail.

Re: [Freesurfer] Qt platform and lta_convert error

2024-09-29 Thread fsbuild

External Email - Use Caution

 You may be missing packages on your system freesurfer needs to run if you 
did not install freesurfer with the .deb package installer   You can 
download the 7.4.1 Ubuntu 22 installer 
from,https://secure-web.cisco.com/1Tsk98POal2iEABYPOiUI6g759awF8BwGwOezDnsIYQGXn7nRqihwblPId9Mn-msNCkXCJihkb1N83BX4oDxKz5_vnyb_1k-P-1t4_UGpxdERCw1a5XEs9jos31S1z1ERWvjj1pDM03grURcadF-dVFaVOHugFVs9ckG1SW2qC_cYIB8_nY64Qvf9CvggGCoOwzgviRO4hM6d2LuZtE9NAx8KSgzV95Lvns5L89l0_pSWFPoWRl1Fni7aj7xwOrlwgVtnCmzdMvh6UocDDWFjCH0zfTuZC8qeHoG3L4pWhbBsNhO20m6ob97jU4mNK2VrFY3dj7Wf5nn_sYDmZXupYw/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Fpub%2Fdist%2Ffreesurfer%2F7.4.1%2Ffreesurfer_ubuntu22-7.4.1_amd64.deb
… change directories to where you downloaded the file …
… as root … $ apt install ./freesurfer_ubuntu22-7.4.1_amd64.deb… or as 
non-root user with sudo privileges …$ sudo apt install 
./freesurfer_ubuntu22-7.4.1_amd64.deb
… setup the freesurfer environment …$ export 
FREESURFER_HOME=/usr/local/freesurfer/7.4.1$ source 
$FREESURFER_HOME/SetUpFreeSurfer.sh 
freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460 Setting up 
environment for FreeSurfer/FS-FAST (and FSL)FREESURFER_HOME   
/usr/local/freesurfer/7.4.1FSFAST_HOME       
/usr/local/freesurfer/7.4.1/fsfastFSF_OUTPUT_FORMAT nii.gzSUBJECTS_DIR   
   /usr/local/freesurfer/7.4.1/subjectsINFO: 
/home/rd521/matlab/startup.m does not exist ... creatingMNI_DIR     
      /usr/local/freesurfer/7.4.1/mni
… check lta_convert is found and that it can at least run and display its help 
output …$ which 
lta_convert/usr/local/freesurfer/7..4.1/bin/lta_convert$ lta_convert 
—help
- R.
On Sep 28, 2024, at 13:40, Mohammad Amin Khodadadegan 
 
wrote:External Email - Use 
Cautionwhen I ran freeview ,I 
have encounter with this error:freeviewThis application failed to start because 
no Qt platform plugin could be initialized. Reinstalling the application may 
fix this problem.
Available platform plugins are: eglfs, linuxfb, minimal, minimalegl, offscreen, 
vnc, wayland-egl, wayland, webgl, xcb.
Aborted (core dumped)

when I run the reconstruction command,I encounter with this error:
fs-check-version --s subj04 --o /tmp/tmp.oDwgAcSat Sep 28 20:00:24 +0330 2024
setenv SUBJECTS_DIR /home/ubuntu/freesurfer/subjectscd 
/home/ubuntufreesurfer/bin/fs-check-version --s subj04 --o 
/tmp/tmp.oDwgAc-rwxrwxr-x 1 1623927 1623927 18565 Jun 14 2023 
freesurfer/bin/fs-check-version
freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460$Id$Linux 
freesurferubuntu 5.15.0-122-generic #132-Ubuntu SMP Thu Aug 29 13:45:52 UTC 
2024 x86_64 x86_64 x86_64 GNU/Linuxpid 6375Current FS Version 
freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460Subject does not have a 
bstampfile, copying freesurfer/build-stamp.txtSubject FS Version: 
freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460No constraints on 
version because REQ=UnSet and FsVerFile=NotThere#@#% fs-check-version match = 
1fs-check-version DoneINFO: SUBJECTS_DIR is 
/home/ubuntu/freesurfer/subjectsActual FREESURFER_HOME 
/home/ubuntu/freesurferLinux freesurferubuntu 5.15.0-122-generic #132-Ubuntu 
SMP Thu Aug 29 13:45:52 UTC 2024 x86_64 x86_64 x86_64 GNU/Linuxlta_convert: 
Command not found.ERROR: Executable 'lta_convert -all-info failed! Is it 
missing from the distribution?'
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://secure-web.cisco.com/1jDQNFEChA6RnfhuCrwzZtv1Q1DkBnjuzgRahazq22iw7z039XCe3LEwbUq2Xi2VYcx7N5isgolfAxAQNoUI8pYb3xtI5AnyTOvMBuxWhjk2w7gQVc8sMDfra94kR4n2S86MmhGIq87v_PQiX3GLRYi_lWGMzS5qrws0wi8s7ZKv3W5UP43wYrd3fqjjKgd_MrEsfkrvQ24O5Zszm6SOchQ8Xhb21M9gA2m-ZL20rWvvDiq10LVqHT4azmgg0omcSTONsGt6ADI27G24naCN8zA3ARdTSe0EXvkn6geT738X4RmKilkT_3dbC4fxFu8ZOmGUSG3xDOabwQjAHc1uM3w/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is 
addressed.  If you believe this e-mail was sent to you in error and the e-mail 
contains patient information, please contact the Mass General Brigham 
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline 
 .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail.

[Freesurfer] dev builds available for rocky Linux and silicon MacOS (M1, M2, M3 processors)

2024-09-27 Thread fsbuild

External Email - Use Caution

 In response to requests for freesurfer on Rocky8, Rocky9 linux and 
silicon macs (with M1, M2, M3 processors), there are updated, relatively stable 
development builds, i.e., builds that have gone thru some testing, available 
from 
https://secure-web.cisco.com/1GcRpXukAZA_u5fux2mIvH7rGNj6Iwz7089dTqiW5XwIhCZuUbWxVqf-6oCwWiVZQXesKe78vEf2S7KszGBvPhRZVhE94zz-FoiDRvOCDFwV5VJ1OgUtcYibgP6v1tN-qnAm9chKNyNQwKVD4Mskez4AN1U7xu7ai6VIue5LNbDCcMqcXgqQ5ZCg8iq-19sgC3F4n0OHwCPLFQFYWNt0OBWKHNgI5fGhbkJsmmO6Wf6xLPelfhLAP6FwByA_ZZMhJJ2EwefBdzkc5CN7mnK3a12UBp6B9BDsmmzasX6AWAKDE8mMKaO0Wmg8DmWB6cf3XVdB0e70G09woaDyALplF4A/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Fpub%2Fdist%2Ffreesurfer%2Fdev%2Fstable%2F
For Rocky8 or Rocky9 Linux, it should work to install the 
rpm, freesurfer-Rocky8-7.0.0-dev.x86_64.rpm
For MacOS on Apple silicon machines with an M1, M2, M3 processor, you can try 
the .pkg installer, freesurfer-macOS-darwin_arm64-dev.pkg.  This has 
been tested on MacOS Monterey, Ventura and Sonoma, BUT NOT Sequoia which was 
just released.
Please let us know if you run into issues.
- R.

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is 
addressed.  If you believe this e-mail was sent to you in error and the e-mail 
contains patient information, please contact the Mass General Brigham 
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline 
 .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail.

[Freesurfer] fresurfer on silicon macs (was Re: Trying to run freeview via Docker/XQuartz and it just aborts

2024-09-20 Thread fsbuild

External Email - Use Caution

Try downloading and installing the development build for the silicon Mac
from,https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev/freesurfer-macOS-darwin_arm64-dev.pkgWe
don’t really support running/debugging X-Windows applications like freeview
thru docker back to the host. For the case where freeview does not run
natively, many people choose a VM image with its own built in X-server, e.g.,
run VirtualBox on Windows.
There are however ubuntu debian package installers located in the same
directory as the mac package listed above, i,.e., there is an Ubuntu 22 .deb
installer. If you don't use the linux install tools to install the .deb
package, then you will likely be missing system libraries.
- R.

On Sep 20, 2024, at 14:36, Belakovski, Nickolai

wrote:External Email - Use
CautionHello all,
I'm just getting started with Freesurfer so please forgive me if I'm missing
something basic, but basically my setup is like this:
I'm on an M3 Mac and I'd like to run FreeSurfer. Since there's arm/x86
compatibility issues I'm trying to run it inside of an x86_64 docker image of
Ubuntu 22.04. I've downloaded the relevant .tar.gz, mounted it inside my docker
and I've installed all the various packages I need to run freeview (basically I
tried to run freeview and every time it complained about a shared lib not found
I'd install the relevant package), but now I've gotten to a point where I try
to run freeview and it just says "Aborted" and that's it.
I have a license.txt at FREESURFER_HOME and I've run source SetUpFreeSurfer.sh,
but basically I'm stuck at this point. I can run freeview -h and get the help
message. I can run freeview --verbose, but this also just results in an
"Aborted" message and that's it.
Is there anything else I can do to debug? The "Aborted" message unfortunately
doesn't give me much to go on 🙁
For the sake of completeness I'll just make a note that I should be able to run
this through Docker. I've installed x11-apps and run xeyes in the same
container in which I'm trying to run freeview and it works, so I don't think
that's the part it's choking on. Also for completeness here's a list of the
packages I had to apt-get install: libgomp1, libgl1, libglib2.0-0, libqt5gui5,
and I also had to export LIBGL_ALWAYS_INDIRECT=1 for some reason.
Thanks very much for your help,Nickolai BelakovskiBiomedical Software
EngineerBioMedical Engineering and Imaging Institute (BMEII)Icahn School of
Medicine at Mount Sinai
___Freesurfer mailing
listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] Running Freeview from Ubuntu (on WSL)

2024-09-19 Thread fsbuild

External Email - Use Caution

 

It would be good to know what version of Ubuntu you 
are running in WSL.   You can see that in the Ubuntu linux terminal 
window with the command below, and you should see something like the 
following ...

  

$ cat /etc/os-release

PRETTY_NAME="Ubuntu 22.04.5 LTS"

NAME="Ubuntu"

VERSION_ID="22.04"

VERSION="22.04.5 LTS (Jammy Jellyfish)"

VERSION_CODENAME=jammy

ID=ubuntu

ID_LIKE=debian

HOME_URL="https://www.ubuntu.com/";

SUPPORT_URL="https://help.ubuntu.com/";

BUG_REPORT_URL="https://bugs.launchpad.net/ubuntu/";

PRIVACY_POLICY_URL="https://www.ubuntu.com/legal/terms-and-policies/privacy-policy";

UBUNTU_CODENAME=jammy

  

- which in this case indicates Ubuntu 22.

  

I would also check you used the Ubuntu 22 .dev installer package from, 

  
https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/7.4.1/freesurfer_ubuntu22-7.4.1_amd64.deb
- and installed it from wherever you downloaded it to on the Ubuntu system with 
the command,

  

$ sudo apt install ./freesurfer_ubuntu22-7.4.1_amd64.deb



If you didn't use that installer, then the system may be missing xcb related 
files it needs to run Qt, etc.



If you got that Qt error even after the freesurfer .deb package install 
completed with no errors, then you could try the commands,



$ xhost +local:

$ sudo apt-get install --reinstall libxcb-xinerama0



Please note you need a license.txt file for freeview to find.  You can 
put that in your $HOME directory on linux and set the environment 
variable FS_LICENSE to point to it



  $ export FS_LICENSE=$HOME/license.txt

$ head -1 $FS_LICENSE

y...@somewhere.com    <-  email address you used to 
reigster via the form, 



Then try running freeview again (with no arguments to see if it can open an 
empty window). 
$ freeview

  

- R.

  


On 9/19/24 17:31, Barsotti, Ercole (john-barso...@uiowa.edu) wrote:






  External Email - Use 
Caution

  
Just re-upping this message in case anyone has any ideas. :)

  


  

  
Hi all,

  


  

  
I've successfully downloaded Freesurfer version 7.4 and can run its 
commands, with the exception of Freeview. I downloaded and installed 
Xming, like the FreeSurfer instructions tell you 
(https://freesurfer.net/fswiki/FS7_wsl_ubuntu),
 but this does not seem to work, either. I am using Ubuntu on a Windows 
computer. I get the following error when I run the freeview command :

  


  

  
This application failed to start because no Qt platform plugin could be 
initialized. Reinstalling the application may fix this problem.

  


  

  
Available platform plugins are: eglfs, linuxfb, minimal, minimalegl, 
offscreen, vnc, wayland-egl, wayland, wayland-xcomposite-egl, 
wayland-xcomposite-glx, webgl, xcb.

  


  

  
Aborted

  


  

  
Best,

  


  

  
John


  
  From: Barsotti, Ercole 

Sent: Thursday, September 19, 2024 12:21 AM

To: freesurfer@nmr.mgh.harvard.edu 

Subject: Running Freeview from Ubuntu
 
  


  

Hi all,





I've successfully downloaded Freesurfer version 7.4 and can run its 
commands, with the exception of Freeview. I downloaded and installed 
Xming, like the FreeSurfer instructions tell you 
(https://freesurfer.net/fswiki/FS7_wsl_ubuntu),
 but this does not seem to work, either. I am using Ubuntu on a Windows 
computer. I get the following error when I run the freeview command :





This application failed to start because no Qt platform plugin could be 
initialized. Reinstalling the application may fix this problem.





Available platform plugins are: eglfs, linuxfb, minimal, minimalegl, 
offscreen, vnc, wayland-egl, wayland, wayland-xcomposite-egl, 
wayland-xcomposite-glx, webgl, xcb.





Aborted





Any ideas?





Best,





John
  




  

  
  ___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is 
addressed.  If you believe this e-mail was sent to you in error and the e-mail 
contains patient information, please contact the Mass General Brigham 
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline 
; .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail. 




___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is 
addressed.  If you believe

Re: [Freesurfer] FreeSurfer License Error

2024-09-18 Thread fsbuild

External Email - Use Caution

Since the last release of freesurfer 5.X in 2014, the encryption
libraries on linux systems have changed such that the licenses downloaded for
the current 7.X
releases,https://surfer.nmr.mgh.harvard.edu/fswiki/rel7downloads- cannot work
with 5.X.
If you were previously using 5.X on an old linux system, then you could run it
with the license file that worked for you on that system in a container or VM
running whatever that OS was - hosted on a current version of Linux like
Rocky8, Ubuntu 22, etc.
Otherwise, I suggest you download and install the 7.4.1 release via the link
above. The license file you downloaded should work with that.
- R.

On Sep 18, 2024, at 20:25, Barsotti, Ercole
wrote:External Email - Use
CautionHi all,
I've downloaded Freesurfer version 5.3 and signed up for a license. However,
when I try to run the example:
mri_convert sample-001.mgz sample-001.nii.gz
I get the following error:
ERROR: Invalid FreeSurfer license key found in license file
/home/john/freesurfer/license.txt
I'm not sure what to do here as I have the license file in the correct place
and thought that I had obtained it correctly.
Best,
John___Freesurfer mailing
listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] Ongoing issue with Mac

2024-09-13 Thread fsbuild

External Email - Use Caution

I mistkamely put the .tgz archive for the Intel Mac instead of its ,pkg file in 
the red box in the screenshot.

- R.

On Sep 13, 2024, at 22:35, fsbuild <fsbu...@contbay.com> 
wrote:External Email - Use 
Caution When you navigate 
in a browser to,https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev/- 
you choose to download the installer package for either an Intel processor Mac 
(freesurfer-macOS-darwin_x86_64-dev.pkg) or a Silicon Mac with an M1, M2, M3 
chip (freesurfer-macOS-darwin_arm64-dev.pkg).
My browser preferences are set to ask whether or not to download a file when 
clicking on a link (see screenshot).  You may not see that if your browser 
is set to block pop-up windows, or you might have some other setting blocking 
downloads, but I can download either package file.  Those files can be 
refreshed periodically, so you may have to reload the web page in your browser 
if you have not looked at it recently. But the link should always work.
After you have downloaded the .pkg installer and clicked on it to install as 
described in the previous maill, you should check freeview can open an empty 
window from the terminal, i.e., don’t try to display and volumes or surfaces.
You should see something like what’s listed below when setting up the 
freesurfer environment in the terminal window.
$ bash$ export FREESURFER_HOME=/Applications/freesurfer/dev$ source 
$FREESURFER_HOME/SetUpFreeSurfer.sh 
freesurfer-macOS-darwin_x86_64-dev-20240909-9ca95c6     <—— 
this is from the install of the Intel Mac .pkgSetting up environment for 
FreeSurfer/FS-FAST (and FSL)FREESURFER_HOME.       
/Applications/freesurfer/devFSFAST_HOME           
     /Applications/freesurfer/dev/fsfastFSF_OUTPUT_FORMAT   
 nii.gzSUBJECTS_DIR               
  /Applications/freesurfer/dev/subjectsMNI_DIR         
                
 /Applications/freesurfer/dev/mni
$ which freeview/Applications/freesurfer/dev/bin/freeview$ freeview   
                      
                      
        <—— this should open an empty freeview window
If you get the empty window, then freeview is basically working.
- R.

On Sep 13, 2024, at 20:24, Alisha Davis <davis.alisha1...@gmail.com> 
wrote:   External Email - Use Caution 
   

Hello,

I sent an email regarding issues with not being able to get the newest version 
(or any version, really) of freesurfer to run on my Mac due to the fact that no 
update can handle MacOS version 14.5. I just received another email from Henry 
that was sent to an individual having a similar issue, and the link for the 
download does not work for me yet again. I keep receiving messages that the 
server cannot be found. I can get the download onto my Mac, but every time I 
open an MRI, the program immediately crashes. Im not sure if there is another 
link to try or one with a server that can be found, but any help would be 
appreciated!

Cheers,
Alisha

___
Freesurfer mailing list
freesur...@nmr.mgh.harvard..edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

<mac_pkg_download.png>___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is 
addressed.  If you believe this e-mail was sent to you in error and the e-mail 
contains patient information, please contact the Mass General Brigham 
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline 
<https://www.massgeneralbrigham.org/complianceline> .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail.

[Freesurfer] Freesurfer 7.4.0 and CUDA versions (was Re: (no subject))

2024-09-10 Thread fsbuild

External Email - Use Caution

 The 7.4.0 release contains the python distribution all the python scripts 
(including mri_synthseg) were tested with (on CentOS 8, 7; Ubuntu 22, 20 18). 
 That python includes tensorflow 2.12.0 which is documented to support up 
thru Cuda 11.8.   If you look at all the cuda libraries you will see their 
major release numbers range from 8-11.  Since older libraries may be 
backwards compatible, I suggest you try installing Cuda 11 on your system and 
see if it is recognized.
- R.

On Sep 9, 2024, at 22:31, Matthew Lynch  
wrote:External Email - Use 
Caution
I run this command: 

mri_synthseg --i /mnt/p/test/test-t2-3mm.nii --parc --robust --o /mnt/p/test

and it fails with the following (partial) error message:

Node: 'model_3/unet_conv_downarm_0_0/Conv3D'
DNN library is not found.

which I assume means it cannot access the appropriate the CuDNN library.

I have installed

GPU: nvidia geforce RTX 3050 Ti (4Gb)
WSL2
Linux kernel: 5.15.153.1-microsoft-standard-WSL2 (after recent wsl --update)
CUDA Version 12.6
Windows Nvidia Driver version 560.94
CuDNN Version 9.4.0 installed in WSL, with libraries located 
in /lib/x86_64-linux-gnu

However, freesurfer's tensorflow seems to point to its own cudnn libraries in:
/usr/local/freesurfer/7.4.0/python/lib/python3.8/site-packages/nvidia/cudnn/lib

including

libcudnn.so.8 

which I assume is CuDNN version 8, and may not be compatible with CUDA 12.6?

Is there a way I can get freesurfer's script to use the CuDNN 9.4.0 that are 
installed globally on the WSL system?  Any other suggestions on what might 
be causing this error and how to fix it?

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is 
addressed.  If you believe this e-mail was sent to you in error and the e-mail 
contains patient information, please contact the Mass General Brigham 
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline 
 .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail.

Re: [Freesurfer] Installer for Silicon M1, M2, M3 Macs (was Re: Freesurfer for MacOS))

2024-09-10 Thread fsbuild

External Email - Use Caution

Single (left) click on the link to download.  Then after the file is on 
your machine, e.g., in the Downloads folder, right click and hold and select 
the option for installer.app (default). 
On Sep 10, 2024, at 12:21, Alisha Davis <davis.alisha1...@gmail.com> 
wrote:External Email - Use 
CautionWhen I right-click on 
that link, I do not get the option to download with the installer.app. Are 
there any other prerequisite steps to this?

Cheers,Alisha
On Sep 9, 2024, at 4:56 PM, fsbuild <fsbu...@contbay.com> 
wrote:External Email - Use 
Caution If you are using a 
Silicon Mac with an M1, M2, M3 chip, then please download and install the arm64 
freesurfer development .pkg installer via the link, 
freesurfer-macOS-darwin_arm64-dev.pkg
Right click on the file freesurfer-macOS-darwin_arm64-dev.pkg and select 
“Open with —> installer.app (default)” which should bypass some of the 
security warnings.  Then follow the prompts to install (you will need to 
enter an admin password).
Then setup the freesurfer environment as usual, setting FREESURFER_HOME, 
sourcing the setup script.  Using this installer should avoid any error 
messages with “illegal instruction" from running the Intel binaries, e.g., from 
the 7.4.1 release.
- R.

On Sep 9, 2024, at 19:19, Alisha Davis <davis.alisha1...@gmail.com> 
wrote:   External Email - Use Caution 
   

Hello,

My name is Alisha Davis, and I have been using Freesurfer over the past few 
weeks for an MRI project but have encountered a few issues due to the version 
of my computer. Is there a plan to release a newer version of Freesurfer 
compatible with newer MacOS versions, or should I resort to reverting the 
update on my computer? I look forward to hearing back from you.

Thank you,
Alisha Davis

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is 
addressed.  If you believe this e-mail was sent to you in error and the 
e-mail contains patient information, please contact the Mass General Brigham 
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline 
<https://www.massgeneralbrigham.org/complianceline>; .

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is 
addressed.  If you believe this e-mail was sent to you in error and the e-mail 
contains patient information, please contact the Mass General Brigham 
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline 
<https://www.massgeneralbrigham.org/complianceline> .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail.

[Freesurfer] Installer for Silicon M1, M2, M3 Macs (was Re: Freesurfer for MacOS))

2024-09-09 Thread fsbuild

External Email - Use Caution

 If you are using a Silicon Mac with an M1, M2, M3 chip, then please 
download and install the arm64 freesurfer development .pkg installer via the 
link, 
freesurfer-macOS-darwin_arm64-dev.pkg
Right click on the file freesurfer-macOS-darwin_arm64-dev.pkg and select 
“Open with —> installer.app (default)” which should bypass some of the 
security warnings.  Then follow the prompts to install (you will need to 
enter an admin password).
Then setup the freesurfer environment as usual, setting FREESURFER_HOME, 
sourcing the setup script.  Using this installer should avoid any error 
messages with “illegal instruction" from running the Intel binaries, e.g., from 
the 7.4.1 release.
- R.

On Sep 9, 2024, at 19:19, Alisha Davis  
wrote:   External Email - Use Caution 
   

Hello,

My name is Alisha Davis, and I have been using Freesurfer over the past few 
weeks for an MRI project but have encountered a few issues due to the version 
of my computer. Is there a plan to release a newer version of Freesurfer 
compatible with newer MacOS versions, or should I resort to reverting the 
update on my computer? I look forward to hearing back from you.

Thank you,
Alisha Davis

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is 
addressed.  If you believe this e-mail was sent to you in error and the e-mail 
contains patient information, please contact the Mass General Brigham 
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline 
 .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail.

Re: [Freesurfer] installation on Linux server incompatible with python2?

2024-09-09 Thread fsbuild

External Email - Use Caution

You could try first installing rocky8, then install freesurfer, then
*upgrade* the machine to rocky9, though you still may not have python2 after
the upgrade. We have not run into any issues so far running the
freesurfer rocky8 binaries on rocky9.
You could try using the —skip-broken switch when you install the RPM directly
on rocky9.
You could try downloading/building python2 directly on the Rocky9 machine,
i.e., see this thread with same issue on
CentOS9,https://stackoverflow.com/questions/71256853/how-do-i-install-python2-on-centos-9-stream
- R.
On Sep 9, 2024, at 17:48, Gowin, Joshua
wrote:External Email - Use
CautionHello FreeSurfer
community, We are trying to install FreeSurfer on a new
server that uses Rocky Linux 9.4 (Blue Onyx). Unfortunately, python2 is not
available on this Linux version, but we believe it is necessary to run
FreeSurfer.Are there possible FreeSurfer builds that do not require python2? Or
would it be better to run FreeSurfer from a container image based on Rocky 8,
which still has Python2 available?Or, are there other solutions that would be
better for us? We’d be grateful for any suggestions for our set
up. Josh ___Freesurfer
mailing
listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] Using a newer version of FS for longitudinal processing

2024-09-08 Thread fsbuild

External Email - Use Caution

This from the bottom of the 
page, https://surfer.nmr.mgh.harvard.edu/fswiki/rel7downloads- R.Important 
Note: When processing a group of subjects for your study, it is essential 
to process all your subjects with the same version of FreeSurfer, on the same 
OS platform and vendor, and for safety, even the same version of the OS. While 
we continue to work to ensure that results match across platforms, there are 
none-the-less system-level libraries that are OS dependent. An exception to 
this rule is that you may view and edit files across any platform or version, 
and run some post-processing tools (outside the recon-all stream) if you check 
with us first (for instance you may run the longitudinal processing with newer 
versions).- R.
On Sep 8, 2024, at 18:28, Bronwyn Overs  
wrote:External Email - Use 
CautionHi Freesurfer mailing 
list,I have over 600 structural MRI images, across three time-points, for which 
cross-sectional processing was completed on a Linux server using Freesurfer 
v5.3. That server is now closing down and we need to process these images using 
the longitudinal processing stream. Is it viable to process all of the 
longitudinal base and long images on a different system using a newer version 
of Freesurfer?
Kind regards,

Bronwyn OversResearch Assistant
Neuroscience Research Australia
Margarete Ainsworth Building
Barker Street Randwick Sydney NSW 2031 Australia
M 0411 308 769 T +61 2 9399 1725
neura.edu.au 

Twitter | Facebook | Subscribe


___
Freesurfer mailing list
freesur...@nmr.mgh..harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is 
addressed.  If you believe this e-mail was sent to you in error and the e-mail 
contains patient information, please contact the Mass General Brigham 
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline 
 .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail.

Re: [Freesurfer] License issues

2024-09-04 Thread fsbuild

External Email - Use Caution

The system you are running freesurfer 5.3 on likely uses older
system libraries that are incompatible with reading current 7.X licenses.
Or 7.X licenses use different (newer) encryption libraries found only on
more recent linux systems. So a license file you download now is not
expected to work on a system where 5.3 runs with its original license. If
you still need to run 5.3 (released in 2013/2014), then you should run it on
the system where it works using its original license from that time period.
If that system is not available, then you could try hosting a CentOS
virtual machine with Freesurfer 5.3 installed on the Linux system where you run
7.4.1. You can download a compressed archive of a VirtualBox CentOS disk
image with Freesurfer 5.3 installed
from,https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.3.0/freesurfer-Virtualbox-linux-x86-stable-pub-v5.3-full.vdi.gz
You would need to install the VirtualBox application on your current Linux
machine to run it.
We discourage posting license files to public lists.
- R.
On Sep 4, 2024, at 03:27, Le Prieult, Yéléna

wrote:External Email - Use
CautionGood
morning, I’m using the TASH toolbox for my project and the
recommended version of freesurfer for this toolbox is 5.3. I used freesurfer
7.4.1 for the recon-all command, not knowing I needed a different version for
the rest of the processing. I used a license that I downloaded month ago and it
worked perfectly for freesurfer 7.4.1 but this license doesn’t work with
freesurfer 5.3. I downloaded a new license and it didn’t work. I tried changing
the permission of access on the license.txt, checked the license key, set
properly all environments as FREESURFER_HOME and SUBJECTS_DIR, etc and
everything is in order but it still doesn’t work. I even redownloaded another
license and tried again but I still encounter the same error:

ERROR: Invalid Freesurfer license key found in license file
/usr/local/freesurfer/license.txt

If you are outside the NMR-Martino Center, go
to https://surfer.nmr.harvard.edu to get a valid license file (it’s
free). If you are inside the NMR-Martinos Center, make sure to osurce the
standard environment.

Attached to this email you can have a look over the license I have. Thank
you in advance for your reply. Best
regards, Yéléna ___Freesurfer
mailing
listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] When release a version for ubuntu24?

2024-09-02 Thread fsbuild

External Email - Use Caution

 We should have a development build on Ubuntu 24 available in the near 
future.
- R.

On Sep 2, 2024, at 04:49, Chunling Hu  
wrote:External Email - Use 
CautionHi, group.I am using 
ubuntu24 now, but the latest FreeSurfer version is only suitable for ubuntu22. 
I wonder when you will release a version for ubuntu24?
Thanks,Hu Chunling___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr..mgh.harvard.edu/mailman/listinfo/freesurfer

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is 
addressed.  If you believe this e-mail was sent to you in error and the e-mail 
contains patient information, please contact the Mass General Brigham 
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline 
 .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail.

Re: [Freesurfer] Help with samseg

2024-08-30 Thread fsbuild

External Email - Use Caution

If you are working on a silicon (not Intel) Mac with an M1, M2, M3 processor, 
then try downloading and installing the development build of freesurfer for the 
silicon 
Mac,https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev/freesurfer-macOS-darwin_arm64-dev.pkgNow
 you may not get the same numerical results with this newer 2024 build compared 
to the 7.3.2 release from 2022, but you will get any/all the latest 
updates/fixes with the 2024 build.
- R.
On Aug 30, 2024, at 19:20, Cacciaguerra, Laura, M.D., Ph.D. 
 
wrote:External Email - Use 
CautionHello everyone,I am 
trying to segment MS lesions with "samseg" (FreeSurfer version 7.3.2), but it 
ends immediately with the following error:
"zsh: illegal hardware instruction  run_samseg --input T1.nii --input 
T2.nii  --lesion"
Have tried to run the command without the option --lesion and it works, so I 
guess the error is somehow linked to that option?
Thank you in advance for your help,All the 
best,Laura___Freesurfer mailing 
listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is 
addressed.  If you believe this e-mail was sent to you in error and the e-mail 
contains patient information, please contact the Mass General Brigham 
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline 
 .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail.

Re: [Freesurfer] Ubuntu 24.04 compatibility? (libc6 < 2.36, libncurses5)

2024-08-16 Thread fsbuild

External Email - Use Caution

 We are aware that changes to the system libraries in Ubuntu 24 prevent 
installing packages, e.g., freesurfer, that otherwise install in Ubuntu 22. 
  The plan is to start development builds of Freesurfer on Ubuntu 24 after 
this years point release of Freesurfer.   Ubuntu 22.04 LTS was made 
generally available in April of 2022 with the standard 5 year support cycle 
from Canonical.
- R.

On Aug 16, 2024, at 18:36, Hunter Buchanan 
 
wrote:External Email - Use 
CautionHi all! Do we know if a 
version of Freesurfer compatible with Ubuntu 24.04 is planned for the near 
future?
Attempting to install the 22.04 .deb file on 24.04 shows that 
dependency libncurses5 is unavailable (manually installing a 
previous version may fix this) and that libc6 < 2.36 is required, 
though 2.39 is already installed (this is the tough one).
If a 24.04 compatible release is not expected in the near future, do we know of 
any temporary fixes to get Freesurfer working? Or are we SOL on new servers for 
now?
Thanks in advance!___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is 
addressed.  If you believe this e-mail was sent to you in error and the e-mail 
contains patient information, please contact the Mass General Brigham 
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline 
 .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail.

Re: [Freesurfer] recon-all terminates at fix topology rh step

2024-08-16 Thread fsbuild

External Email - Use Caution

 You’re using the 7.2.0 release from 2021 whereas the latest release is 
7.4.1 from 2023.   Unless you have to stick with the older release because 
floating point math results could differ with a newer one, then you could try 
downloading and installing the 7.4.1 release from the links under “7.4.1 
Release” at the top of the page,

https://surfer.nmr.mgh.harvard.edu/fswiki/rel7downloadsOr try just running the 
subject that fails with the 7.4.1 release to see if it makes a difference.
- R.

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is 
addressed.  If you believe this e-mail was sent to you in error and the e-mail 
contains patient information, please contact the Mass General Brigham 
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline 
 .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail.

Re: [Freesurfer] mri_easyreg

2024-08-15 Thread fsbuild

External Email - Use Caution

 When you setup the freesurfer 7.4.1 environment from the terminal, check 
you see the output below when running bash shell from the terminal.  If 
you see all the same output, then it should at least work to get the help info 
from the command…
$ bash

$ export FREESURFER_HOME=/usr/local/freesurfer/7.4.1$ source 
$FREESURFER_HOME/SetUpFreeSurfer.sh 
freesurfer-linux-centos7_x86_64-7.4.1-20230613-7eb8460      
<—- MAKE SURE YOU SEE THIS EXACT LINESetting up environment for 
FreeSurfer/FS-FAST (and FSL)FREESURFER_HOME   
/usr/local/freesurfer/7.4.1FSFAST_HOME       
/usr/local/freesurfer/7.4.1/fsfastFSF_OUTPUT_FORMAT nii.gzSUBJECTS_DIR   
   /usr/local/freesurfer/7.4.1/subjectsMNI_DIR       
    /usr/local/freesurfer/7.4.1/mniFSL_DIR       
    /usr/pubsw/packages/fsl/current
… then check you see this output ...
$ which mri_easyreg/usr/local/freesurfer/7.4.1/bin/mri_easyreg$ file `which 
mri_easyreg`/usr/local/freesurfer/7.4.1/bin/mri_easyreg: Bourne-Again shell 
script, ASCII text executable$ which 
fspython/usr/local/freesurfer/7.4.1/bin/fspython$ fspython --versionPython 
3.8.13
… now the help option should work …
$ mri_easyreg —help
… you may see some warning messages before the help text if your machine does 
not support cuda for tensorflow …
usage: mri_easyreg [-h] [—ref REF] [--ref_seg REF_SEG] [--flo FLO] [--flo_seg 
FLO_SEG] [--ref_reg REF_REG] [--flo_reg FLO_REG] [--fwd_field FWD_FIELD] 
[--bak_field BAK_FIELD] [--affine_only]          
         [--threads THREADS]
EasyReg: deep learning registration simple and easy
optional arguments:  -h, --help           
 show this help message and exit  --ref REF       
      Reference image .  --ref_seg REF_SEG     
Reference SynthSeg segmentation (will be created if it does not exist).  
--flo FLO             Floating image.  
--flo_seg FLO_SEG     Floating SynthSeg segmentation (will be created 
if it does not exist).  --ref_reg REF_REG     (optional) 
Registered referenced.  --flo_reg FLO_REG     (optional) 
Registetred floating images (in space of reference).  --fwd_field 
FWD_FIELD                    
    (optional) Forward field  --bak_field BAK_FIELD    
                    
(optional) Inverse field  --affine_only         
(optional) Skips nonlinear part  --threads THREADS     
(optional) Number of cores to be used. Default is 1. You can use -1 to use all 
available cores
If you see all the above, then maybe some command options/parameters are 
causing mri_easyreg to fail.  I’ve asked the mri_easyreg developer to look 
at your command.
- R.
On Aug 15, 2024, at 10:23, Sara Ponticorvo <ponti...@umn..edu> 
wrote:External Email - Use 
CautionHello,so the command I 
used is: mri_easyreg --ref MP2RAGE_uni_resampled_2mm.nii.gz --flo 
sub017_ute_anat.nii.gz --ref_seg mprage_seg.nii --flo_seg ute_seg.nii 
The output I get is:Illegal instruction

I also tried putting the absolute path to the files, but I get the same output. 
And, I also tried to get the help (but I'm not sure if there is one) by typing 
mri_easyreg --h and mri_easyreg --help, but I get the same Illegal instruction 
output..I'm running it on CentOS Linux 7 server.
The output from cat /etc/redhat-releaseCentOS Linux release 7.9.2009 (Core)
Thank you for your help!SaraOn Thu, Aug 15, 2024 at 12:45 AM fsbuild 
<fsbu...@contbay.com> wrote:

Hello Sara,
Please send along the terminal output from running the command so we can see 
the error.
Maybe you could also let us know what version of CentOS you are running, e.g., 
also include the output from,
$ cat /etc/redhat-release

- R.

On Aug 14, 2024, at 15:32, Sara Ponticorvo <ponti...@umn.edu> wrote:
External Email - Use 
Caution
Hi Freesurfer experts!I am trying to use mri_easyreg. I've installed freesurfer 
v7.4.1 on my centos machine but when I try to run mri_easyreg I've "Illegal 
instruction" message. Do you have any suggestion on how to solve it?
Thank you,Sara ___
Freesurfer mailing list
freesur...@nmr.mgh..harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

-- Sara Ponticorvo, PhDCenter for Magnetic Resonance ResearchUniversity of 
Minnesota2021 6th St. S.E.Minneapolis MN 55455 (USA)phone: +1 612 626 2001 
(front-desk)e-mail: ponti...@umn.edu
___Freesurfer mailing 
listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is 
addressed.  If you believe this e-mail was sent to you in error and the e-mail 
contains patient information, please contact the Mass General Brigham 
Compliance HelpLine at https:

Re: [Freesurfer] mri_easyreg

2024-08-14 Thread fsbuild

External Email - Use Caution

Hello Sara,
Please send along the terminal output from running the command so we can see 
the error.
Maybe you could also let us know what version of CentOS you are running, e.g., 
also include the output from,
$ cat /etc/redhat-release

- R.

On Aug 14, 2024, at 15:32, Sara Ponticorvo  
wrote:External Email - Use 
CautionHi Freesurfer experts!I 
am trying to use mri_easyreg. I've installed freesurfer v7.4.1 on my centos 
machine but when I try to run mri_easyreg I've "Illegal 
instruction" message. Do you have any suggestion on how to solve it?
Thank you,Sara ___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is 
addressed.  If you believe this e-mail was sent to you in error and the e-mail 
contains patient information, please contact the Mass General Brigham 
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline 
 .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail.

Re: [Freesurfer] freesurfer version 6 on Debian

2024-08-13 Thread fsbuild

External Email - Use Caution

 Debian 9 looks like it was the current version when Freesurfer 6 was 
released in 2017 for CentOS6 and MacOS.    But even if Freesurfer 6 
runs on Debian 9, it’s not expected to run on current versions of Debian or 
CentOS because of system library changes that can break binary backwards 
compatibility.    I suggest you create a CentOS6 VirtualBox VM or 
Docker container and then install/run Freesurfer 6 in that.   You should 
be able to use Virtualbox or Docker to host CentOS6 on current versions of 
Linux, MacOS and Windows.
- R.

On Aug 13, 2024, at 14:57, Gregory Book  
wrote:External Email - Use 
CautionIs there a way to 
install freesurfer6 on Debian? I see only CentOS packages available for 
freesurfer6.
Or, is there a way to build from source on 
Debian?___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is 
addressed.  If you believe this e-mail was sent to you in error and the e-mail 
contains patient information, please contact the Mass General Brigham 
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline 
 .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail.

Re: [Freesurfer] Hypothalamic region segmentation

2024-08-09 Thread fsbuild

External Email - Use Caution

 Hello Raphaela,
You probably installed the Intel Mac binaries to run on your Silicon Mac with 
an M1, M2, or M3 arm64 chip.  But not all Intel code will run on the newer 
arm64 Macs.   You instead need to download and install the Silicon Mac 
nightly freesurfer build.
To remove your current freesurfer install, you can try running the uninstall 
script from the command line under what you set FREESURFER_HOME to,
$ cd $FREESURFER_HOME$ sudo bash uninstall.sh
Once you have removed your current freesurfer installation, you can download 
and try installing the development build arm64 
pkg, https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev/freesurfer-macOS-darwin_arm64-dev-20240805.pkg
Right click with the mouse on the .pkg file and select “Open with —> 
install.app (default)".  Then follow the prompts in the installer windows.
You should be using the python distribution included in the Freesurfer 
distribution under $FREESURFER_HOME/python.  The mri* commands that need 
python should automatically run it when those commands are issued on the 
command line, in a script, etc.  You can also run it directly from the 
command line as “fspython” after you set FREESURFER_HOME and source the setup 
file for the shell you run in the terminal window, e.g.,
$ export FREESURFER_HOME=/Applications/freesurfer/dev$ source 
$FREESURFER_HOME/SetUpFreeSurfer.sh… output deleted …$ which fspythonfspython
The freesurfer python (fspython) is python 3.8 and should include the necessary 
packages including a tensorflow package.  If you use a different python, 
e.g., 3.11, with different package versions installed, etc.., then commands may 
not run or work correctly.
- R.
On Aug 9, 2024, at 15:39, Raphaela C  
wrote:External Email - Use 
CautionDear the Freesurfer 
community,
I am trying to segment the sub-ROIs of the hypothalamus using the 
mri_segment_hypothalamic_subunits tool, but I keep getting an error that says 
"zsh: illegal hardware instruction." I ran the recon-all command first and then 
this segmentation command.
The first time I tried to run this command, it didn't prompt me to install 
tensorflow, so I manually installed it, but I'm still getting this error. 
I am using a Mac OS Sonoma 14.1, python 3.11.6, and tensorflow  Would 
appreciate any advice.
Thanks!___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is 
addressed.  If you believe this e-mail was sent to you in error and the e-mail 
contains patient information, please contact the Mass General Brigham 
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline 
 .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail.

Re: [Freesurfer] Older tksurfer and tkmedit (FS version 5.0.0) fail to launch: glut issue?

2024-08-07 Thread fsbuild

External Email - Use Caution

 For something released on CentOS4 like the 5.0.0 release mentioned in 
your email, you are probably better off running CentOS4 in a VM or container 
which in turn is hosted on a machine running a current/supported version of 
Linux, e.g., Rocky8, Rocky 9, Ubuntu 22, Ubuntu 24, etc.   That is the 
usual way to preserve such an old OS environment.  The version of OpenGL 
or system libraries something was built against on CentOS4 back in 2011 are not 
expected to be backwards compatible or run on a current system with an OS some 
3+ revisions newer.
There are virtualbox disk image archives for Freesurfer 5.0.0 (*.vdi) files 
underhttps://surfer.nmr.mgh.harvard..edu/pub/dist/freesurfer/5.0.0/The complete 
7.5G .vdi file 
is,https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.0.0/freesurfer-Virtualbox-linux-x86-stable-pub-v5.0.0-full.vdiIf
 you have root/admin privileges to install VirtualBox on some machine, then you 
should be able to import that .vdi file into VirtualBox  - which is likely 
a CentOS4 VM.  I believe Freesurfer 5.0.0 will already be installed there. 
 You could also try running the VirtualBox application on a Mac or Windows 
machine.
- R.
On Aug 7, 2024, at 19:19, Raij, Tommi A.  
wrote:Dear Surfers,
I am trying to launch tksurfer/tkmedit in the stable 5_0_0 environment in the 
Martinos network, but this fails with glut segmentation errors. FS version 6 
tksurfer works on the same machine and data, but I need to create some figures 
that match version 5. We already tried with a different user and a few years 
older linux box, same issues. Any suggestions would be greatly 
appreciated! For example, is there a variable that we could set to point 
to an older OpenGL version? (My LD_LIBRARY_PATH has not been set, and my 
PATH does not include anything pointing to /usr/lib or /usr/lib64)
Details:
on machine rukki (locally at terminal):
setenv USE_STABLE_5_0_0source /usr/local/freesurfer/nmr-stable50-envcd 
$MY_SUBJECTS_DIR
Checking version:freesurfer...You are running this version of FreeSurfer:  
freesurfer-Linux-centos4_x86_64-stable-v5.0.0-20110319
echo $FREESURFER_HOME
/usr/local/freesurfer/stable5_0_0
cp -r $FREESURFER_HOME/subjects/fsaverage $MY_SUBJECTS_DIR/.chmod -R 777 
fsaverage
[rukki:sphsm10-ffx] (nmr-stable5.0-env) tksurfer fsaverage lh inflated
subject is fsaveragehemi    is lhsurface is inflatedsurfer: current 
subjects dir: <$MY_SUBJECTS_DIR>surfer: not in "scripts" dir ==> using 
cwd for session rootsurfer: session root data dir ($session) set to:surfer: 
    <$MY_SUBJECTS_DIR>Reading image info 
<$MY_SUBJECTS_DIR>/fsaverage)Reading 
<$MY_SUBJECTS_DIR>/fsaverage/mri/orig.mgzsurfer: Reading header info from 
/<$MY_SUBJECTS_DIR>/fsaverage/mri/orig.mgz[rukki:sphsm10-ffx] 
(nmr-stable5.0-env)
 after which there is no screen output. The file xdebug_tksurfer was 
generated:
[rukki:sphsm10-ffx] (nmr-stable5.0-env) more .xdebug_tksurfer
SegfaultInitializing glutxDebug stack (length: 1)  00:   00: 
Initializing glut
SegfaultInitializing glut[rukki:sphsm10-ffx] (nmr-stable5.0-env)
[rukki:sphsm10-ffx] (nmr-stable5.0-env) echo $DISPLAY:3
setenv DISPLAY :0 does not fix the issue (results in GLUT: Fatal Error in 
tksurfer.bin: could not open display: 0)
I also tried fsaverage4, fsaverage5, fsaverage6, and bert, copied from the same 
folder into my $SUBJECTS_DIR, same result.
The issue is not specific to tksurfer:
tkmedit -f fsaverage/mri/T1.mgz

===ERROR: A segfault has occurred. This is not 
your fault,  : but is most likely an unrecoverable error and has  : 
made the program unstable.  :  : Please send the contents of the file 
.xdebug_tkmedit  : that should be in this directory 
to freesurfer@nmr.mgh.harvard.edu  :  : Now exiting...  
:[rukki:sphsm10-ffx] (nmr-stable5.0-env)
more .xdebug_tkmedittkmedit started: Wed Aug  7 16:54:21 2024
  tkmedit.bin -f fsaverage/mri/T1.mgz 
$Id: tkmedit.c,v 1.341..2.1 2010/08/04 20:47:28 greve Exp $ $Name: stable5_0_0 
$Set user home dir to ($MY_SUBJECTS_DIR)Set subject home dir to 
fsaverage/mri/T1.mgz
SegfaultImporting volume with MRIreadxDebug stack (length: 5)    
      04: Volm_ImportData( this=0x3447db0, 
isSource=./fsaverage/mri/T1.mgz )          04: 
Importing volume with MRIread        03: LoadVolume( 
iType=0, isName=fsaverage/mri/T1.mgz, ibConform = 0 )      
  03: Reading data into volume      02: ParseCmdLineArgs( 
argc=3, argv=tkmedit.bin )      02: Loading volume 
fsaverage/mri/T1.mgz    01: main()    01: Parsing command 
line arguments  00:   00: [rukki:sphsm10-ffx] 
(nmr-stable5.0-env)
My OpenGL version:[rukki:sphsm10-ffx] (nmr-stable5.0-env) glxinfo | grep 
"OpenGL version"
OpenGL version string: 4.6.0 NVIDIA 550.54.14The other machine we tried had 
OpenGL version 4.6.0 NVIDIA 535.54.03
Thank you!
Best regards,
Tommi

--- Tommi Raij, MD, PhDDirector, TMS Clinical Research
MGH/MIT Athinoula A. Martinos Center for Biomedical Imagin

Re: [Freesurfer] Tksurfer and freeview

2024-08-07 Thread fsbuild

External Email - Use Caution

 The tksurfer command is deprecated and no longer supported.  You 
could try using freeview directly or run tksurferfv which may use some of the 
same options as tksurfer, but runs freeview instead. 
  

$ tksurferfv --help

  

This is a script that runs freeview with arguments like tksurfer.

Not all tksurfer functionality is replicated.

  

tksurferfv subject hemi surface ...

  

-tksurfer : use tksurfer instead of freeview

Can have multiple annotations

  

-all : load white, pial, inflated

-vgl : runs freeview with /usr/pubsw/bin/vglrun

-no-vgl : does not run freeview with /usr/pubsw/bin/vglrun

-no-outline : do not show annots as outline

-vtxno vtxno : put cursor on vtxno on the first surface

-neuro : use neurological orientation instead of radiological

-rotate-around-cursor (-rca) : in 3d view, rotate around cursor (use -no- to 
turn off)

-linear, -linearopaque, -piecewise, -min_to_max (default) : overlay heat scale

--keep-sphere-vol-geom : do not ignore sphere volume geometry when loading 
sphere

  




On 8/7/24 16:01, Hengameh (hennn2...@gmail.com) wrote:



  Hi Ed,

I am currently encountering the same issue.
Could you please assist in fixing this issue?Thank you for your help.
Hengameh  Sent from Mail for Windows 




___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is 
addressed.  If you believe this e-mail was sent to you in error and the e-mail 
contains patient information, please contact the Mass General Brigham 
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline 
 .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail.

Re: [Freesurfer] mri_easyreg --help error: zsh : illegal hardware instruction mri_easyreg --help

2024-08-05 Thread fsbuild

External Email - Use Caution

Hello Yaozhi,
You probably installed the Intel Mac binaries to run on your Silicon Mac with
an M1, M2, or M3 arm64 chip. But not all Intel binaries will run on the
newer arm64 Macs. If you want to run that command you will need to
download and install the silicon Mac nightly freesurfer build.
To remove your current freesurfer install, you can try running the uninstall
script from the command line under what you set FREESURFER_HOME to,
$ cd $FREESURFER_HOME$ sudo bash uninstall.sh
Once you have removed your current freesurfer installation, you can download
and try installing the arm64
pkg, https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev/freesurfer-macOS-darwin_arm64-dev-20240805.pkg
Right click with the mouse on the .pkg file and select “Open with —>
install.app (default)". Then follow the prompts in the installer windows.
- R.
On Aug 5, 2024, at 21:45, Yang, Yaozhi
wrote:External Email - Use
CautionHello FreeSurfer
Developers,
I am trying to use easyreg from the paper--- A ready‑to‑use machine learning
tool for symmetric multi‑modality registration of brain MRI and the paper says
that I can use freesurfer to get the easyreg function. But after I download
freesurfur in my macbook, and run mri_easyreg –-help on the terminal, I get the
error saying that zsh : illegal hardware instruction mri_easyreg --help. So can
you help me with that? How can I use easyreg method? Thank you very much!
Best,Yaozhi___Freesurfer mailing
listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] Not able to install Matlab Runtime (MCR)

2024-07-09 Thread fsbuild

External Email - Use Caution

 It looks like /tmp is running out of space (which can be a separate 
partition much smaller than the boot partition) to the point where the matlab 
installer cannot use it.  You can check that with,
$ cd /tmp$ df -h .
You should be able to delete anything under /tmp as nothing permanent should be 
written there.
- R.
On Jul 9, 2024, at 04:02, Himanshu Joshi  
wrote:External Email - Use 
CautionDear list,I am trying to 
install matlab runtime environment (MCR) in $FREESURFER_HOME/freesurfer by 
using fs_install_mcr R2019b. the error is mentioned below:
(Jul 09, 2024 12:00:11) The following error was detected while 
installing 3p/mpich2_glnxa64:

/tmp/tmp.YZJEtKG8O6/install-target/v97/bin/glnxa64/smpd (No space left on 
device)

Would you like to retry installing 3p/mpich2_glnxa64?  If you press No, 
the installer will exit without completing the installation.  More 
information can be found at /tmp/mathworks_MBIAL.log
(Jul 09, 2024 12:00:11) Exiting with status -1
(Jul 09, 2024 12:00:11) End - Unsuccessful.
Finished
R2019b installed successfully in /home/MBIAL/freesurfer/MCRv97

We have enough space on / filesystem:
Filesystem             Size  Used Avail Use% 
Mounted on
/dev/mapper/rhel-root   50G   43G  7.4G  86% /
devtmpfs               252G     0 
 252G   0% /dev
tmpfs                  252G   
21M  252G   1% /dev/shm
tmpfs                  252G   
19M  252G   1% /run
tmpfs                  252G   
  0  252G   0% /sys/fs/cgroup
/dev/sda2              497M  219M 
 279M  44% /boot
/dev/mapper/rhel-home  3.3T  2.3T  961G  71% /home
tmpfs                   51G   
48K   51G   1% /run/user/1003

Kindly suggest the needful
Thanks and Regards
-- 
Dr Himanshu Joshi
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is 
addressed.  If you believe this e-mail was sent to you in error and the e-mail 
contains patient information, please contact the Mass General Brigham 
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline 
 .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail.

Re: [Freesurfer] Freeview cannot be opened (MacOS)

2024-07-02 Thread fsbuild

External Email - Use Caution

 

If you prefer to run the last stable release (7.4.1),
 then I suggest downloading and installing the Intel binary package 
installer, 
https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/7.4.1/freesurfer-macOS-darwin_x86_64-7.4.1.pkg ;
  To bypass some security prompts, right click on the package file and 
then choose "open will default ..."

You should check the path, but I think you would set things up in the (bash) 
shell as,
$ export FREESURFER_HOME=/Applications/freesurfer/7.4.1... source the 
environment setup script ...$ source $FREESURFER_HOME/SetUpFreeSurfer.sh

  

If you don't mind running the latest development build (which can be 
unstable), then you can try the native arm64 binary package installer 
via the link, 
https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev/freesurfer-macOS-darwin_arm64-dev-20240327.pkg  ;
 Install the same way via right click as listed above.  Then check the 
path, e.g,
$ export FREESURFER_HOME=/Applications/freesurfer/dev... source the environment 
setup script  ...$ source $FREESURFER_HOME/SetUpFreeSurfer.sh

  

Assuming you have your license file setup, e.g., to be read via 
FS_LICENSE environment variable with license.txt under your home 
directory,

$ export FS_LICENSE=$HOME/license.txt

  

- then it should work to run freeview.  I would first try running 
freeview from the shell command line w/o any arguments to see if it opens an 
empty window.  

$ freeview

  

Then exit and try it again with a known to be good volume, 

$ freevivew $SUBJECTS_DIR/bert/mri/brain.mgz

  

- R.



On 7/1/24 13:42, Melih Keskin (keskinmeli...@gmail.com) wrote:



  External Email - Use 
Caution
  Hi,
I am trying to open Freeview 
using my M1 Macbook (Monterey version 12.5). I am posting the error it 
gives me below. I followed the steps from the below thread but none of 
the solutions worked (mainly changing the privacy settings and getting a
 new Freesurfer 
license). https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg70979.html

Is there a solution to this problem as of 2024?
Thank you in advance,Melih






2024-07-01
 20:41:03.731 Freeview[70874:2969887] *** WARNING: Method 
userSpaceScaleFactor in class NSView is deprecated on 10.7 and later. It
 should not be used in new applications. Use convertRectToBacking: 
instead. 
[0]PETSC ERROR: 

[0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, probably 
memory access out of range
[0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger
[0]PETSC ERROR: or see 
http://www.mcs.anl.gov/petsc/petsc-as/documentation/troubleshooting.html#Signal[0]PETSC
 ERROR: or try http://valgrind.org on linux or man libgmalloc on Apple to find 
memory corruption errors
[0]PETSC ERROR: configure using --with-debugging=yes, recompile, link, and 
run 
[0]PETSC ERROR: to get more information on the crash.
[0]PETSC ERROR: - Error Message 

[0]PETSC ERROR: Signal received!
[0]PETSC ERROR: 

[0]PETSC
 ERROR: Petsc Release Version 2.3.3, Patch 13, Thu May 15 17:29:26 CDT 
2008 HG revision: 4466c6289a0922df26e20626fd4a0b4dd03c8124
[0]PETSC ERROR: See docs/changes/index.html for recent updates.
[0]PETSC ERROR: See docs/faq.html for hints about trouble shooting.
[0]PETSC ERROR: See docs/index.html for manual pages.
[0]PETSC ERROR: 

[0]PETSC ERROR: Unknown Name on a darwin12. named Melihs-MacBook-Pro.local by 
keskin Mon Jul  1 20:41:01 2024
[0]PETSC ERROR: Libraries linked from 
/usr/pubsw/packages/petsc/2.3.3-p13-64b/src/petsc-2.3.3-p13/lib/darwin12.2.0-c-opt
[0]PETSC ERROR: Configure run at Mon Dec 17 15:29:35 2012
[0]PETSC
 ERROR: Configure options --with-debugging=no --with-cc=gcc --with-fc=0 
--download-f-blas-lapack=0 --download-mpich=1 --with-mpi=1 --with-x=0 
--with-gnu-copyright-code=0 --with-shared=0 COPTFLAGS=-O3 
CXXOPTFLAGS=-O3 FOPTFLAGS=-O3
[0]PETSC ERROR: 

[0]PETSC ERROR: User provided function() line 0 in unknown directory unknown 
file
[unset]: aborting job:
application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0

  

  
  ___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is 
addressed.  If you believe this e-mail was sent to you in error and the e-mail 
contains patient information, please contact the Mass General Brigham 
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline 
; .
Please note that this e-mail is not secu

Re: [Freesurfer] freesurfer as module

2024-07-02 Thread fsbuild

External Email - Use Caution

 My understanding is that it is up to the sysadmins who run a cluster to 
choose how to present and configure the apps they host whether it be thru 
modules, spack, or other tools.  We don't track how cluster admins do 
that, but you could ask the helpdesk for the cluster you are going to use 
(which presumably lists there is some version of freesurfer already available 
on the cluster).  Most have online documentation stating how to run their 
apps.
I have used Freesurfer in the past on the SDSC cluster, and according to their 
web pages, they do use 
modules,https://www.sdsc.edu/support/user_guides/expanse.html#software

- R.

On 7/1/24 14:55, Dong, Yilei (yid...@health.ucsd.edu) wrote



  

  
Hi Freesurfer Developers, 

  


  

  
If Freesurfer is available as a module on a computer cluster, is it 
still necessary to source/configure the freesurfer module in a .bashrc 
script on Linux? 

  


  

  
Sincerely,

  
Yilei 




  

  
  ___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is 
addressed.  If you believe this e-mail was sent to you in error and the e-mail 
contains patient information, please contact the Mass General Brigham 
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline 
; .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail. 





___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is 
addressed.  If you believe this e-mail was sent to you in error and the e-mail 
contains patient information, please contact the Mass General Brigham 
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline 
 .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail.

Re: [Freesurfer] freesurfer launching error

2024-06-18 Thread fsbuild

External Email - Use Caution

 The info at the end of this posting about updating sshd_config in your 
Linux image might be helpful if you have not already tried it (enable 
X-forwarding, use local X11 
 host)https://stackoverflow.com/questions/62363023/x11-forwarding-from-wsl2-fails
You could try updating WSL which I don’t think is updated along with the OS. 
 Looks like that command is,
 wsl —update
Some postings indicate that WSL2 now has its own X-server, WSLg,  but that 
it does not work as well 
as VcXsrv,https://www.reddit.com/r/wsl2/comments/172urvu/wsl2_no_longer_requires_xserver_few_questions/
Another posting about using WSLg 
is,https://superuser.com/questions/1682522/gui-apps-not-working-in-wsl2-for-windows-11
If the above does not work, maybe try uninstalling and re-installing VcXsrv.
-R.
On Jun 18, 2024, at 06:56, yunus soleymani  
wrote:External Email - Use 
Cautionhi 
everyone, recently after a major Windows 11 update, I can not launch 
Freeview in my WSL Ubuntu machine despite having VcXsrv working in the 
background,  and encountered the following error:
 QXcbConnection: Could not connect to display 10.255.255.254:0Could not 
connect to any X display.

do you have any idea to troubleshoot this error?
I appreciate any help you can provideBest,Yunus


___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is 
addressed.  If you believe this e-mail was sent to you in error and the e-mail 
contains patient information, please contact the Mass General Brigham 
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline 
 .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail.

Re: [Freesurfer] Help: when will the next version of FreeSurfer become available?

2024-06-11 Thread fsbuild

External Email - Use Caution

 We have no current reports about security issues with the FS release. 
  An address using the string fsbuild will email you directly so you can 
respond to only that address if you would like to report an issue.  Please 
check you spam folder.  PLEASE DO NOT POST AND/OR DISCUSS SECURITY ISSUES 
ON THE PUBLIC FREESURFER LIST.
- R.
On Jun 11, 2024, at 16:03, Tran, Kevin (NIH/NIMH) [E] 
<kevint...@mail.nih.gov> 
wrote:External Email - Use 
CautionHi,We have been 
pressured by our IT Security team to address some of the vulnerabilities (e.g., 
OpenSSL) they found in FreeSurfer 7.4.1. I am wondering if you could share 
with us when would the next version of FreeSurfer become 
available?  Thanks,--Kevin TranData 
ScientistThe National Institutes of HealthNIMH, Laboratory of Brain and 
Cognition10 Center Drive, Room 4C215Bethesda MD 
20892-1366kevint...@mail.nih.govWork:(301)435-4936 
Cell:(301)755-3715___Freesurfer 
mailing 
listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is 
addressed.  If you believe this e-mail was sent to you in error and the e-mail 
contains patient information, please contact the Mass General Brigham 
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline 
<https://www.massgeneralbrigham.org/complianceline> .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail.

Re: [Freesurfer] Bug in mri_convert reslice-like with 4D images

2024-06-06 Thread fsbuild

External Email - Use Caution

 It could help to see the core dump file.  If you are on a Mac it 
will probably display it.  If you are on Linux and you have core dumps 
enabled on the system, then you have to look in the logs.
- R.

On Jun 6, 2024, at 15:56, Iglesias Gonzalez, Juan E. 
 wrote:Dear FS experts,We get a 
segfault when I try to resample images with the command:mri_convert input.mgz 
output.mgz -rl reference..mgz when reference.mgz has multiple frames 
(e.g., a RGB volume). Any idea of why this is happening?Cheers,/Eugenio 
(&Stefano & 
Pranav)___Freesurfer mailing 
listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is 
addressed.  If you believe this e-mail was sent to you in error and the e-mail 
contains patient information, please contact the Mass General Brigham 
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline 
 .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail.

Re: [Freesurfer] License for FreeSurfer 5.x

2024-05-30 Thread fsbuild

External Email - Use Caution

 Hello Rafa,
If you take a look under,
https://secure-web.cisco.com/1dfxSJC8JWSEz6n8dSa8oPi0pnwDlx9137h03BernH-2Q8eEewwiAs4_GzpGOKvQvQC3n0ZOzmkJywWiQhnZl1hp8X7dZz_1b5uzmyic7OwNcW2wT_tLTYBwTq7v44waYGSfLHYoIXzuMDkmGJA6TeCJ_9t27l3YBR-gpCXTlMtZF6idOKlosZWj2TboaTbNTa-2UVNDaP1QVnDMKL2k-1o-69Ad91inM7hvvpuulSQAEHZ1lC5a1j7TRDozna0YW0RVMmfzF2iGFstFaTgEkHv8sobpaqiseS6E2qOmt3jDk23FmAIoaOC5-ESz-TTffGyO92TI6lzK9RXiu4wG1ZQ/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Fpub%2Fdist%2Ffreesurfer%2F5.3.0%2F
- you will see there is a Virtual Box ..vdi file for the 5.3.0 release, 
https://secure-web.cisco.com/1RcGOCq2p6BYFO6rvNlcGnNuDdMKQaAC7luBVOPnx9yiqMFJA6ldXhzlTOSfcVrRQGXzGhINxzFYo_JFhUypqciLq0LT4ZY-Ej3rL9p3wkwBPeYEfHGq9AiHGiD2C0N98VtG4hc0VSzwpgRnRpJ6f9w-X4Xo1dSP2R3LnChQtmfool5KrHnUWDbLkb1vE0TFUS6fjdZ1tsu1z5xr1F2lavylYNlz2ZGk5HaShaPW2GiFl6LrnQs21aADXH1VPVwRm-kOwK06on5aY6IxxmAmgEFD3NCqLf7JJ1iNrGBd6YA5dWU-EDU6IjSiXqPepvPPlw0VeA5IOo6xGxQZmdvb8FA/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Fpub%2Fdist%2Ffreesurfer%2F5.3.0%2Ffreesurfer-Virtualbox-linux-x86-stable-pub-v5.3-full.vdi.gz
- but I think that Virtual Box image will be running CentOS6 (or some old 
version of CentOS).  At that time we did not build or provide releases for 
Ubuntu linux.  The version of CentOS in the VM and Ubuntu12 may use 
different versions of glibc so I’m not sure the packages with 5.3.0 binaries 
listed above will run on Ubuntu12.
We advertise the following caveat about switching to newer/different OS 
versions, or upgrading to a different (newer) Freesurfer release built with 
different compilers.  Either of those changes will likely produce some 
difference in floating point math results.
Important Note: When processing a group of subjects for your study, it is 
essential to process all your subjects with the same version of FreeSurfer, on 
the same OS platform and vendor, and for safety, even the same version of the 
OS. While we continue to work to ensure that results match across platforms, 
there are none-the-less system-level libraries that are OS dependent. An 
exception to this rule is that you may view and edit files across any platform 
or version, and run some post-processing tools (outside the recon-all stream) 
if you check with us first (for instance you may run the longitudinal 
processing with newer versions).
But if it’s not an issue for you to run on an old version of CentOS instead of 
Ubuntu linux, then your best bet is to try and run the existing .vdi file 
listed above in the VirtualBox client - which you would need to download and 
install on your current Linux machine.
-R.
On May 30, 2024, at 12:34, Rafael Navarro  
wrote:External Email - Use 
CautionHello everyone, 
I am working with a neuroimage model that uses the FreeSurfer 5.3 version as 
preprocessing (only autorecon-I). I have tried to install Freesurfer 5.3, but 
after reading previous messages in the mailing list It seems the license file 
format changed from FreeSurfer 5.3 to 6.0 due to an update of the 
Ubuntu libcrypt. Do you think that migrating the autorecon-I from v5.3 to 
v6.0 might affect the final results? Is there any alternative? Does a docker 
container running Ubuntu 12 with FreeSurfer 5.3 could work? Is still possible 
to get a license with the old format? 
Regards! Rafa 
Navarro  ___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://secure-web.cisco.com/1rQmyzrBzuTiOfJNym0JFZOqwWej3pdzcvkhiXJWLyPV3LsBO78Sckiyswwi-yJokkHY1sD0opu5tST_Akl8z1RORzTFOyikM2YOTdGKEwmy4I0jdMyVTYHf8Kp6fOVeZvHBKcHEUo6ImPXqZjJtwUaEdYkQtac0ynK9EvXl01GfnpnjpOESlGNRBdvtQmAJqLOA7fUFlECFJo_PJASqTJ_uWmkbXrlwAFc-ecjNJmrh264MKbwuCGtxHRmw6IEDg10xgF_03mzKdsdw_2hy97M1RheGhFjjRFD2Hv8xd4L4RfcsRLMHYwLQTLODtFo87dhlDPN65CmgzEIiX4S_PlA/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is 
addressed.  If you believe this e-mail was sent to you in error and the e-mail 
contains patient information, please contact the Mass General Brigham 
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline 
 .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail.

Re: [Freesurfer] SynthSR problem

2024-05-28 Thread fsbuild

External Email - Use Caution

 Some commands such as mri_synthsr in previous releases, e.g., 7.4.1, use 
code built with Intel processor specific instructions that cannot run on an arm 
processor, i.e., there is not full backwards binary compatibility in that case 
using the Rosetta emulation environment on MacOS.  Hence the “illegal 
instruction” error.
We do have a (more recent) development build on a Silicon Mac you can download 
via the link, 
https://secure-web.cisco.com/1lWnZREm3JXXMeuMNsb_hOkyb2ipaBFlFN8u43RUzyQ6-cBpOY1HIvsCJ6Yq6EQh42_qmFVn3W8VSBrcGCmTg1ofVHbrA2XH36Cn4xi0k0HeHZVG0YnMoLQ3iwly-wQYbTnjuDPGI2_jkWwFekN96gabVpPg7pllxMYINHzHVpD4U0GWvGdRnvnpcF2h_20PzI5XZhR0U699zA75vyBnJ9JMLld3H6EOz4Da1ljgW2DZ4BTntHXXrwaxQGIKb20hYndKoBJXrJ5iMVGBQFIsS5ncHwrxaWBVUOxU0oVfR7vaKhPPuFTx8SKXbcUDiBX4ZlexIztClTwjKgklKIusnHA/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Fpub%2Fdist%2Ffreesurfer%2Fdev%2Ffreesurfer-macOS-darwin_arm64-dev.pkg
 it has not yet gone the the same testing as done for a release.  
Please let us know if you run into issues trying it.
- R.

On May 28, 2024, at 16:08, Tabasi, Farhad  
wrote:External Email - Use 
CautionHello FreeSurfer 
developers,
I am trying to use mri_synthsr to improve the quality of clinical scans, but 
this is the error I encountered:
Illegal instruction: 4
(I followed the instructions on SynthSR page, using mri_synthsr 
--i input.nii --o output_synthT1.nii command)
FreeSurfer version: freesurfer-darwin-macOS-7.3.2-20220804-6354275OS: macOS 
Ventura (13.2.1) on iMac M1 (116 GB)
This is likely related to binary problems or CPU compatibility (especially with 
M1).Is there any solution to the issue?
Thanks,Farhad
Farhad Tabasi, MD (he/him/his)Postdoctoral ScholarHuman Brain Research Lab,
Department of Neurosurgery,
Carver College of Medicine, University of IowaCell: 
(858)588-2779___Freesurfer mailing 
listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is 
addressed.  If you believe this e-mail was sent to you in error and the e-mail 
contains patient information, please contact the Mass General Brigham 
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline 
 .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail.

Re: [Freesurfer] Group Stats for hipposubfields, brainstem and amygdalar

2024-05-27 Thread fsbuild

External Email - Use Caution

 If you still have the VM setup on your machine, you 
can open a new terminal window and then you should see the Freesurfer 
Environment is setup,

  

FREESURFER_HOME   /home/developer/7.2.0/dev

FSFAST_HOME   /home/developer/7.2.0/dev/fsfast

FSF_OUTPUT_FORMAT nii.gz

SUBJECTS_DIR  
/home/developerfreesurfer/7.2.0/subjects

MNI_DIR   
/home/developer/7.2.0/mni

garnet2[0]:tmp$ ls $FREESURFER_HOME/bin/aparc*

  

The aparc* and aseg* commands should all be in your path, i.e.

  

$ which aparc_stats_aseg

/home/developer/7.2.0/bin/aparc_stats_aseg

  

$ which aparcstats2table

/home/developer/7.2.0/bin/aparcstats2table

  

$ which aparcstatsdiff

/home/developer/7.2.0/bin/aparcstatsdiff

  

$ which aparc2feat

/home/developer/7.2.0/bin/aparc2feat

  

$ which aseg2feat

/home/developer/7.2.0//bin/aseg2feat

  

$ which asegstats2table

/home/developer/7.2.0//bin/asegstats2table

  

$ which asegstatsdiff

/home/developer/7.2.0//bin/asegstatsdiff

  

You should be able to get some info about the commands using the "-h" or help 
option.

  

garnet2[0]:tmp$ aparcstats2table -h

Usage: 

Converts a cortical stats file created by recon-all and or

mris_anatomical_stats (eg, ?h.aparc.stats) into a table in which

each line is a subject and each column is a parcellation. By

default, the values are the area of the parcellation in mm2. The ...

. rest of output deleted 

  

- R.

  



On 5/21/24 07:45, Carina Obermüller (carina.obermuel...@live.at) wrote:



  External Email - Use Caution

Dear Freesurfer team,

I am looking for a group stats command like the asegstats2table and 
aparcstats2table command for hipposubfields, brainstem and amygdalar, but I 
couldn’t find it in the archives. I remember it was mentioned in the recent 
Freesurfer course, but I can’t find it anymore. Could you help me out?
Also more generally, is there an overview page of all the possible group stats 
commands?

Thank you so much in advance for your reply!

Sincerely,

Carina


___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://secure-web.cisco.com/1zf0G1ETkn7CuwsYRmLLhHlYlAkhG2RaT4vLqBGQDlX4KiUh3QuSvrAj3mjN3IM0YzmnHif2TEyZlZfbArMlEIXCuFiC6aqNSsQHHqda-rzL7Yacb2RaJNtWHIP44Kftud3K1IusHvFnV1rDPJOE9HM86gvqJUjsSxTxPhiTCgt3ZCoKKckzt3BhA2KKocTJtqlB__2C1VCOIamqcr3fL2oGxfUyHWuvpGdTjqkOm-SqGlFowP_SQmt75jbIjtFaKGPeDZVgUAi0JxMMgBE3ZBdzyJ0_swBLFTNHTIbaWrjSqrjesHAHK-FqUk92SSlaH/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
The information in this e-mail is intended only for the person to whom it is 
addressed.  If you believe this e-mail was sent to you in error and the e-mail 
contains patient information, please contact the Mass General Brigham 
Compliance HelpLine at 
https://secure-web.cisco.com/1nGDgYhKOmxBKFFUQGUJR-tfzcA07RiW6HdqaGmQhhm7ox9BPMPAmpUSocDnOGcmpfZ9jJcOnM-xBKuUVl5MHQ16rhUnge0I899N_uK05xFoRKkuPthkrVwXx2gaSNBF8ybcuzphkPUPpQXFQZ0XyAniakIW62vtMLyoeuOmZDUPTD0YoTe2AVGLuQqPMOfoBdXTpT1SVDBabJ7Miq1y5ycy7J-tRr4RrGYX5ZjFeJWTrE6SBxjS-ZSExQPEfGTv3r4zZblRmIQSzCTNKCxi_UDfMhRh987IaR91L8p-RfwJYb1-axJIZnY6INieLK_OV/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline
 
 .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail.

Re: [Freesurfer] MAC compatibilty

2024-05-25 Thread fsbuild

External Email - Use Caution

 The Intel binaries should still run on Silicon Macs using the built-in 
Rosetta emulation environment.  So if you want to use an official release, 
then the Intel binaries from the most recent June 2023 7.4.1 release can be 
found here:
https://secure-web.cisco.com/1PlXQxoEX-x05USM5h21mbTgkWDKGf26NwLJXc-0TKpfOiCFIPKTNfixRTstm4lwdFle1ckZQaNDG9K2uXTrL4PgECdRb1kB_7yoS7khQb0ehN9jhQdUEx760OIsW4yS15fGVX2egl-kP-gUfA8mcGgT60fYkpOBtL34Q4XfiQpnY1cyK4Qqix_1L2MqBZwQmqpy77YwZet2977GkKZQWCJJH3Efq_fu4bs31PqnDT7GH0wKw4xpynQgYZqKFDx2AkPPLgjGxEE4pw0Wi67HAZl4XlGt1_52MXZDtYFdwJ-LmwkxE_VdxXa68ba42bxgnpVTNDrEMR3T3qZGRJ5NzYw/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2Frel7downloads
There is however a newer development (non-release) build compiled natively for 
the Silicon (arm64) Macs.  You can find development builds under,
https://secure-web.cisco.com/1bqoWa8LCXJXDBOMIgjvymagPdUuAoVFBzhDkQcCJ8BO0z-AZtSuIBxg3dgBxnDm_R3YCWCP73q0CQsSKFyW2x74gcZTMU-skv2NKEJpxs8JrKVEBT9cduIT3bgaeRqTaKYbAPkmyixKaV3b5DspaTK1FKHuF3XoG-_UI7jDI2Wlh7nRboHjFUkY65GZX8wF1RiHq8O6Lma-thaFJNoIPCW47mSNy_k8BfzB06E6t9dnJ2ebKfeuJvhvRc2jgf4x-yYmD6Q3l6kpMd0APnM1cXP-hxyldsY86BJmBjC1agSZGZgW3NFrcB3Sh836GHFxKKixmeiyxw8GocHHyif1H3A/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Fpub%2Fdist%2Ffreesurfer%2Fdev
- and the current arm64 .pkg file installer is:

https://secure-web.cisco.com/1v7jUCTarAa0YZGcgQjK2FDqKV6MOl2jENY0Cmgh3LS7Tbjl3BBwYxUBU9KrYpFUz3kNsQXeNAsuR87a0V4E9JSverkt5GYgtXxTTr6_bL8FBO9kdzQ99iyRTfPKFsLSMXBpJ4maosVp3cAWGAFzfc4nWl-dxrxBTSHHomvryS8Vyq0T4byXQRjA_3hAvxNL2-uHTW4X4q4Cf89AxweyE8ewSJ9IZUQen4XPJAmNuVMZhYrQIP2iPIgateMIe6ARMmsEORI-tXGrYBL8Hq83RiW-3YwQ7kDJl0sbadpIsRabO9xxP6FCfjbSv4odPFCdyucnownn7fGoh9s7c_EGhyw/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Fpub%2Fdist%2Ffreesurfer%2Fdev%2Ffreesurfer-macOS-darwin_arm64-dev.pkg
- R.

On May 25, 2024, at 04:58, Silvia Montanari  
wrote:   External Email - Use Caution 
   

Good morning, my office needs to buy a new computer and it’s mandatory that it 
can run free surfer properly. I couldn’t really find definitive informations 
about the compatibility with latest Mac machines with M2-M2pro-M3 processors. 
Since I always had Intel, can you help understand which Mac it’s better to have 
in order to not have problems with freesurfer? 

Thank you in advance,
Silvia Montanari

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://secure-web.cisco.com/1qRxeyWkkR5NFNT5R5CKBfscu_bFL-MpZk-peIzi07txHg0QszKKSeXAmk2OfT7CVdYSzcOGYUe8VvTo3gMS29puqn0HVW8LkRRjk03pAM9pUdjujUie76IQ8P0y1R8pviczBHTfkDHH5tI4uPkw3brFRWtl7k5IcFpusYfvZoVnAzN6RKrPvmxEuabrElqg-DEIipzzbZzuyLl4fFUnAsO7-i2ywd6qQtKcRXdzLLGo1NFz0RnrKPz08PuWxKvbE5w5CXLXo4ZktbPktvZ12O8WDo9-G3ELLDM6GSwPU2VKixiyMy61mSKaG7BCbBCO60nhtsPCO8bgjOCjoCrgSbQ/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is 
addressed.  If you believe this e-mail was sent to you in error and the e-mail 
contains patient information, please contact the Mass General Brigham 
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline 
 .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail.

Re: [Freesurfer] MCR install for parcellation

2024-05-09 Thread fsbuild

External Email - Use Caution

Hello Antonio,
With the 7.4.1 release, you can install R2014b or R2019b matlab runtime
environment into the freesurfer tree. Earlier freesurfer releases use
R2014b. I would setup the freesurfer environment first, and then pass in
the value of FREESURFER_HOME on the command line as listed below. Below,
I have shown using R2019b with a linux install of Freesurfer 7.4.1 using bash
shell.
- R.
- - - - -
$ export FREESURFER_HOME=/usr/local/freesurfer/7.4.1
<--- linux install path
$ source $FREESURFER_HOME/SetUpFreeSurfer.sh
<... output deleted ... showing SUBJECTS_DIR and other environment
variables>
$ cd $FREESURFER_HOME/bin
$ sudo FREESURFER_HOME=$FREESURFER_HOME ./fs_install_mcr R2019b
I believe this sets things up (for R2019b) so the libmwm* libraries are
installed under $FREESURFER_HOME/MCRv97/bin/glnxa64. You can try adding
that path (or any path the fs_install_mcr script output recommends) to the
start of LD_LIBRARY_PATH. You should remove any other entries to a
different MATLAB distribution other than the one you actually install.
On May 9, 2024, at 12:45, Antonio Di Renzo
wrote:External Email - Use
CautionMessers FreeSurfer
developers,I dowloaded MCR zip file for linux in /home/vboxuser/Downloads from
MatLab website.I extracted files in new foldern named
Matlab_Component_Runtime_R2014b in Downloads.I am trying to install Matlab
Component Runtime, but the the following command: fs_install_mcr R2014b
does not work.Where can I find the right step by step MCR installation
guide?Thank
you,Antonio___Freesurfer mailing
listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] Problem running recon-all

2024-04-23 Thread fsbuild

External Email - Use Caution

 If you use a shared drive that is formatted in a way that is not 
compatible with the linux (ext3, ext4) file system, e.g., a shared windows 
drive, then running the linux software is not expected to work.  A Windows 
file system does not support soft links, permissions etc. which means recon-all 
will fail when it tries to use soft links to point to files.  So 
SUBJECTS_DIR has to point to a directory you can write to (on a linux file 
system).   Similarly, the linux packaging tools (apt, dpkg, yum, 
rpm) expect to install Freesurfer on to a linux file system in order to set 
permissions, etc.
- R.

On Apr 23, 2024, at 11:50, Gregory Book <gregory.a.b...@gmail.com> 
wrote:External Email - Use 
CautionI did not see that 
message, which is why I posted again. Sorry about that!I will try using the 
package installer. We're using the .tar.gz method because it is located on a 
shared drive, but maybe we'll just need to install it locally if that works.On 
Tue, Apr 23, 2024 at 11:23 AM fsbuild <fsbu...@contbay.com> 
wrote: Did you try the instructions  you were sent yesterday to run 
the actual installer and not use the tar file (which is not an installer) ?- 
R.I would try downloading and running the actual package 
installer,  MailScanner has detected a possible fraud attempt from 
"secure-web.cisco.com" claiming to 
be https://secure-web.cisco.com/1uViOtWTuZtLn_S-t5ZXgvMBVJDZpi3jEUIyVF5p0RkWblvKvIJkFxDXEZA2KSZZuqs200u1U---PlkDbqhzxoTRAOSnSZjJc2956J0XGD_vWI7nfllZOrIm_bHjGKto9WW1iRhjfrAikyAvowOGgQbVSsA6ScAjx6rTlmIWUdT6OyI7IEXl_E0IrZ_kImj52MyATeYxASxc-Ia_3XRMg4pIqKDo72F4tPWwrCiEsim74mHNaLF3XbDs-4dm5LzF2JQxd9OJoAoMR1Uh5lIyVpgAIn2jYEOHi6WfrVXXUT98tHEQUBpG1aTr1JQ5VPwua4FeyBnagpReKK8UhZTwXW_oNSrQHbXDsni3znEjUnhU/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Fpub%2Fdist%2Ffreesurfer%2F7.4.1%2Ffreesurfer_ubuntu22-7.4.1_amd64.debon
 to the target system..  Then change directories to where you downloaded 
the package and try,$ sudo apt install ./freesurfer_ubuntu22-7.4.1_amd64.debI 
cannot guarantee the installer will work as the Debian linux packaging tools 
may find requirements in the Ubuntu package they cannot resolve/satisfy on your 
Debian system.  We don’t test on debian linux.  But the installer 
should notify you if it fails and why that is.On 4/23/24 09:21, Gregory Book 
(gregory.a.b...@gmail.com) 
wrote:External Email - Use 
CautionI recently installed 
freesurfer 7.4.1 on a Debian 12 system (using the Ubuntu 22 .tar.gz). When 
running recon-all, I get the following error:-bash: 
/opt/freesurfer/freesurfer-7.4.1/bin/recon-all: cannot execute: required file 
not foundPaths are all set, and all scripts and executables have execute 
permissions.What might be 
happening?___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" 
claiming to be 
https://secure-web.cisco.com/1-JQYLUxMaRFGVYXQgiVBp3x6S8AOp7o-1GJmVB_WrdMAqwl3fB1_lQt-PAFkfuZUXui9u7sxZxfNq1jrTb_3aWEIJTRhqJpg6Aq-Yo-dSUo15_VLf_8TIsK0B7HaW6_Yw5wpN5MOHEcCWXVfFqOCwy5dKMsq8NAbt8Xnvw5qSqXsirInWlWW_Bnj5DO5NdFk1RmZb1L8tLg1OSuwwg3V8btHEYeq-adBrPYPQ2uBIVESHlZPQXeEy5PUbSa3sf01V-DXmNyJm5DFJjk_DdGoYo4k0x-jHMweEnoRvarnRSoWxu2FJqR4cegbnYWjB3D_wa2z7IEOpe7dJEZPbADfelwACClpr73vA3bwh6fUiQw/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
The information in this e-mail is intended only for the person to whom it is 
addressed.  If you believe this e-mail was sent to you in error and the e-mail 
contains patient information, please contact the Mass General Brigham 
Compliance HelpLine at MailScanner has detected a possible fraud attempt from 
"secure-web.cisco.com" claiming to be 
https://secure-web.cisco.com/1YSC_5-yK_syGsrpbV_FlchsehO6_LZWlIQjx7-t0KMR0zN0SXNDlDD3BEpefbtOu9TfVqmEvpvGVxC_la2nyQyJlqnPWjn02Amaqh4dZtlBs_oEiAPK5TdWNk1UhAt15r5snA3RPwIXbcJD_nV7OpRpsEb5qFdpw2Jx2Wk3Q8Gfyy6jSuXQKzzXbxocCVeLkitY7v5sEL-2NK3E8uCczpzuZ13_5Moy6uVPFBeqtF3-geHpmAlo0BmKiZGei8-rMVeknu5-yyviJD2T_mF20kTSTZuI6ZD3PGOBA2bzXgK7N00F4Wrju4VFBVsUz8K_9o_GbIRnS0wyvgDjTGMPntk7dVbITXddw0zt7fv2-0A0/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline
 <MailScanner has detected a possible fraud attempt from 
"secure-web.cisco.com" claiming to be 
https://secure-web.cisco.com/1_G0ZVPLNmtmKmt_wysLzFxsWKaGnqKJh6r9LMQNommXRwMqy-5yzRA117656DW2Xv9k9XboRAoZaPuMV8QIYnJgk90kJHPWkuVyBMKhfl4EsqE-5atXlBVrfQMxPdCv9Xm9qnwQsiRYcQmNFDhahR3RFHv7DMWI30NOQbWMjBIfoYYnok6u45qd4K1b_ErvWSRcIaI4WxHGx4j2Jo7hh_km3VGPoJ-hh7EcnSK1YT5plFi9SY1BjVS1l4EHuikUJfY5z_EQC54KtwUP7ev5zjCmLmjmBuC3ZsUqVuMNmNS1lydKTdspoDlrKxpUA7txkLpRku9HAHUUVe2WKpsOoYDJ8W6syoW83T2qn7DcdOBs/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline%26gt;
 .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencryp

Re: [Freesurfer] Problem running recon-all

2024-04-23 Thread fsbuild

External Email - Use Caution

 

Did you try the instructions  you were sent yesterday to run the actual 
installer and not use the tar file (which is not an installer) ?

  

- R.

  

  I would try downloading and running the actual package installer, 



 https://secure-web.cisco.com/1mB3zzEt6hQJ2VvtNrO3nW8sgR7_P581WGaaGeCTSIwiN-Z-x8Mtw6Z5nF23uvW00XlyjmsjQtPTwUkHji_2-9LmsBV2L2NfcLNBFy1Gsw0HvQ045CqPAZjAVhMRFnyyvnfw4xOPMnU-gIj1bM4eLgNASRmckkz7PGd6j28HxgvfDZkF1VK3pZSwTcISKqhKHuNQatTZ9vZjaWbY5k7I5N6dvIOuntBKrq-p5rjI7Q9G73EQ-rCrhQLcAOOyFsAtGAF4BJS1Ph12Iri8OA0T7HkE4bJHEf8g0Rde3zzo82KH1VslH5icbSMuRfXtKveMgAUF6jySJNeW6klBJSbUdsw/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Fpub%2Fdist%2Ffreesurfer%2F7.4.1%2Ffreesurfer_ubuntu22-7.4.1_amd64.deb


on to the target system.  Then change directories to where you 
downloaded the package and try,


$ sudo apt install ./freesurfer_ubuntu22-7.4.1_amd64.deb



I
 cannot guarantee the installer will work as the Debian linux packaging 
tools may find requirements in the Ubuntu package they cannot 
resolve/satisfy on your Debian system.  We don’t test on debian 
linux.  
But the installer should notify you if it fails and why that is.


  
  



On 4/23/24 09:21, Gregory Book (gregory.a.b...@gmail.com) wrote:



  External Email - Use 
Caution
  I recently installed freesurfer 7.4.1 on a Debian 12 
system (using the Ubuntu 22 .tar.gz). When running recon-all, I get the 
following error:
-bash: /opt/freesurfer/freesurfer-7.4.1/bin/recon-all: cannot execute: required 
file not found

Paths are all set, and all scripts and executables have execute 
permissions.What might be happening?

  

  
  ___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://secure-web.cisco.com/1SqDEz4wELZL2ecp4LsUGnw8nhV4bVWQUj3TOG5K_ebNudx3R6iUuXOmowBFnwQbTazUGeJ86GE9lot8EPfR02ye7zSRLfESGIXN2opXb08s5Y1BPL0zsBVkvRPbg9fv3Ot5cu_RPWfRjBvrEEBPxLRFh2UV2XVhkhIqW-H0V-vVUCRiAvqS4ub1NZb9fKg3i36ueGHnypbj_mJDRJZbZ9iFYwqA3rrFBtyZqPevhJMsSqZvQq9kgr0TeWzqei95nYzz4NKeiunuhkScbXSC_-ZURnyRj0VlFhDefksa0qvD6yoMBjsJIvJK99W0q4GWxrm7NLxxZCw5zncsYovxqLw/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
The information in this e-mail is intended only for the person to whom it is 
addressed.  If you believe this e-mail was sent to you in error and the e-mail 
contains patient information, please contact the Mass General Brigham 
Compliance HelpLine at 
https://secure-web.cisco.com/1b5TUTVtPusBNEm83E0MNUu7lAF2DA0LT4edaHsGpFUa1lAMlXozLSCv9SMdmHtlq8_cVPm2vf_LUZJxqetaip0AGUxyQFGjm7S-lFR7NPcNBizdj0eUx_RrXhfhq9KgWymKRiov25j1ymEwIJtv180wpVEeAj4pU0vat2kBJODWC8LSGYVh31KihQYUVynWVXh13GA9fLDvFaBCEexzihaYnQr6s53U9AmBGyLDWBw1d3jKAX_vkThs9mgMhv4zKXnECdHp6a0-kRONRXFN6Yru-7_nYdVm7jevHYiAjhXCDTh1_EkufWdZeEcK9veC7KY1OYduSg6ga4jENP4VTtw/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline
 
 .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail.

Re: [Freesurfer] Freeview problems

2024-04-17 Thread fsbuild

External Email - Use Caution

 You can check the post (quoted below) to verify the setup for the 7.4..1 
release.   Instead of running the freeview command as listed in the post, 
you can run the mri_info command with no arguments to get the help info about 
the command line options.  If mri_diff runs and prints out the help 
output, then the issue is likely your command line arguments.
- R..
bash-3.2$ mri_info
USAGE: mri_info fname1   

   --conformed : print whether a volume is conformed stdout
   --conformed-to-min : print whether a volume is conformed-to-min 
stdout
  

SETUP ENVIRONMENT
https://secure-web.cisco.com/1-xQ9e5Z3VTlXilKkcSpNfmxzfXMzCk-PG0p40zknkFsd-OPflitvKnVBlbPqmZOOFVb9VAQ0M1PT82eJ-TQA5l5vXu3cxmiGQ_qMXFYiU6W_jXNSmGaqA3RbGU1beyO26DOuGjlunX7l_t7p3sBnlGCA8WPnPy5fmpsoKV4dY4ITrs3S59UCZ3IberbbCAyXNGPIhR261f_R6V7uFYU-YpjHa3r0hv9PElrVro7lKsGm-JNW6TmXBe6o5armcI5hCwbyu-rAezm9TjIL9J1eeRnkdiZvqDGt6oWMD0j9ILzFiiHj3UZbJHfsC8hr3mZDxdqSJlibJW8p2rTBT4emBQ/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg76743.html

If you setup the Freesurfer environment ... here using bash and not zsh ...
hostname ~ bash
$ export FREESURFER_HOME=/Applications/freesurfer/7.4.1$ source 
$FREESURFER_HOME/SetUpFreeSurfer.sh freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460
 Setting up environment for FreeSurfer/FS-FAST (and 
FSL)FREESURFER_HOME   /Applications/freesurfer/7.4.1FSFAST_HOME  
     /Applications/freesurfer/7.4.1/fsfastFSF_OUTPUT_FORMAT 
nii.gzSUBJECTS_DIR      
/Applications/freesurfer/7.4.1/subjectsMNI_DIR        
   /Applications/freesurfer/7.4.1/mni
 and point FS_LICENSE to your license.txt file, e.g., in your $HOME 
directory 
$ cd$ pwd/Users/myuserid$ ls license.txtlicense.txt$ export 
FS_LICENSE=license.txt$ head -1 license.txt...@somewhere.com  < 
email you used to register
 then try running from the command line  ...
$ freeview $SUBJECTS_DIR/bert/mri/T1.mgz
Please keep in mind you will need to change SUBJECTS_DIR to some other path, 
e.g., $HOME/subjects
$ mkdir -p $HOME/subjects$ export SUBJECTS_DIR=$HOME/subjects
 and put files there if you want to write /modify subject files and data 
since /Applications/freesurfer/7.4.1/subjects is read only by default (not 
intended to be used to write data).
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is 
addressed.  If you believe this e-mail was sent to you in error and the e-mail 
contains patient information, please contact the Mass General Brigham 
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline 
 .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail.

Re: [Freesurfer] FreeSurfer Download and Install Error: Segmentation Fault

2024-04-15 Thread fsbuild

External Email - Use Caution

 If you setup the Freesurfer environment ... here using bash and not zsh 
...
hostname ~ bashThe default interactive shell is now zsh.To update your account 
to use zsh, please run `chsh -s /bin/zsh`.For more details, please visit 
https://secure-web.cisco.com/1RXVOTUqK1IY787C_o3ARLPP6BLZ_gJwBTdWVVnMp01gcO_F-J6H9b6Zq3d5SK5kRaqVP1Dy7gp_ZUzinjn0e1fJiF91lrnT1f-P3z6-4fS0DPdhVFDkHU3VunBCO6PI4W_n_Moh_kpeDUesFuUdMUKJDHyaSJQxz89stfjN4o2S63-wtgXWD69-NcnvfiXHCVemaN-MwXtjWqf_Ob0XZE_DueuAv03mLL7fBehx-acCMOgp9xydtvm8w9mx-wczMuXjDTd3hO0qUCvj5pZKKat0Ct5VKXipXjPJB17x_PK0jh8ATayA_VW0fH_wd9yQf9MLWMtHhE5vJD0-saUcUoN7EGGDqZHMa6GkDpFiw9YQ/https%3A%2F%2Fsupport.apple.com%2Fkb%2FHT208050
$ export FREESURFER_HOME=/Applications/freesurfer/7.4.1$ source 
$FREESURFER_HOME/SetUpFreeSurfer.sh freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460
 Setting up environment for FreeSurfer/FS-FAST (and 
FSL)FREESURFER_HOME   /Applications/freesurfer/7.4.1FSFAST_HOME  
     /Applications/freesurfer/7.4.1/fsfastFSF_OUTPUT_FORMAT 
nii.gzSUBJECTS_DIR      
/Applications/freesurfer/7.4.1/subjectsMNI_DIR        
   /Applications/freesurfer/7.4.1/mni
 and point FS_LICENSE to your license.txt file, e.g., in your $HOME 
directory 
$ cd$ pwd/Users/myuserid$ ls license.txtlicense.txt$ export 
FS_LICENSE=license.txt$ head -1 license.txt...@somewhere.com  < 
email you used to register
 then try running from the command line  ...
$ freeview $SUBJECTS_DIR/bert/mri/T1.mgz
Please keep in mind you will need to change SUBJECTS_DIR to some other path, 
e.g., $HOME/subjects
$ mkdir -p $HOME/subjects$ export SUBJECTS_DIR=$HOME/subjects
 and put files there if you want to write /modify subject files and data 
since /Applications/freesurfer/7.4.1/subjects is read only by default (not 
intended to be used to write data).
- R.On Apr 15, 2024, at 21:55, Angenelle Rosal 
 
wrote:External Email - Use 
CautionHello FreeSurfer 
Developers, I am currently using FreeSurfer 7.4.1 and I am attempting to 
upload the T1 image from subject “bert” using the terminal (I am using MacOS 
Ventura 13.5), as described in the demo video. However, freeview keeps quitting 
unexpectedly showing “2406 Segmentation fault: 11 
$FREESURFER_HOME/Freeview.app/Contents/MAC0S/freeview “$@” when I type in 
“freeview/Applications/freesurfer/7.4.1/subjects/bert/mri/T1.mgz”. When I 
manually open Freeview without the terminal and load such image using the “Load 
Volume” tab, it works fine. I’ve searched the archives list and it might be due 
to the location of my license. However, I believe my license is located in the 
correct file, as it is located in my Freesurfer file 
(/Applications/freesurfer/license.txt). And so, any advice to also solve this 
problem would be greatly 
appreciated! Thanks ___Freesurfer
 mailing 
listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is 
addressed.  If you believe this e-mail was sent to you in error and the e-mail 
contains patient information, please contact the Mass General Brigham 
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline 
 .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail.

Re: [Freesurfer] freesurfer doesn't work

2024-04-13 Thread fsbuild

External Email - Use Caution

If you have not already done so, please make sure your license.txt file
has been setup in the shell for the freesurfer commands to read.
Go to the URL below, fill out the form, and wait for license.txt to be emailed
to the address you provided.
https://secure-web.cisco.com/1S0vdVHQI48_A4EBWTDRa1pv58cpXoGqSkuGFlQee0x1XYr-fPSsM4eHw_WEylrMZxyT6U5ViGv76nFrvLuXJzi4HBwJnBZpfhdbXoRAnkFDpfxJyh710zWgTCqYzqHYfY6myV39Eh5l8mkMgKv-IIKl-7mbrcgdNm58-LvGSR8nwkU9YJEOQuryCauBUfsNsucCK4bB6sg9tImwv0MAELBM_c3UetB20q1H6I__j3P6wWELbVCiJ_c5S334dEbZZQgOENSMQolfi_9moqK1g-FvgnafjL53gKv7w5TmqpI7V0oJ832xMYhY-EpmVnCA7NSx2ow4YDGmg9QN7RfOwEA/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Fregistration.html
Download license.txt file,e.g. into your Downloads folder. Then in
bash or zsh you can do,$ cd $HOME… download license.txt from email into
Downloads folder ...$ mv Downloads/license.txt .$ export
FS_LICENSE=$HOME/license.txt$ head -1 $fs_license...@somewhere.com
<—— email you used to registerYou can add the export command above into your
shell init file so FS_LICENSE will be set when you launch a new terminal window.
- R.
On Apr 13, 2024, at 13:08, 이준하
wrote:External Email - Use
CautionI can't open freesurfer
and I don't know why. It says 'Freesurfer quit unexpectedly'

Re: [Freesurfer] WMH-SynthSeg - Torch module not found

2024-04-11 Thread fsbuild

External Email - Use Caution

 The current nightly build dated April 12th available from 
under,https://secure-web.cisco.com/1eprQplECVjQEgFy-DNvfPnzwSjew2U260XYR6pjQfShhM9gtsn58XZ4YRUlHYleeawzdPreispMAkZ2MQM7djCWtpvLAsdUowgmUhDSJuQv8O_5fefPPEs1LslaJbLvtLiYSihrPpDMqQl8XI-wfA6fvBLvdZGEorSSHkE8HZc964yhAJAU0LYSYOy9cD9hlCMe5NUexf5FlsSHnL5tt8VUWpdEbJ4kGOxPh5yeIs8vl4_Cv8UwrnmG7lIrS6lOu9oUQLQnNBK5VKpADCMYEek0svgu1wUv1NH8cYOpg4jfy9cfhhXCpznkSR99lHGKlu4Wnj2ZdK-iefKmAPd91yQ/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Fpub%2Fdist%2Ffreesurfer%2Fdev%2F-
 should have all the modules as well.
- R.

On Apr 11, 2024, at 10:03, Iglesias Gonzalez, Juan E. 
 wrote:The  idea would be to 
source 7.4.1 and then run:fspython 
 [location_of_FS_dev]/python/packages/WMHSynthSeg/inference.py 
[arguments]Cheers,/Eugenio --Juan Eugenio 
Iglesiashttp://http://secure-web.cisco.com/1Bz_4nONhypuVg0at2yxM7j3iTzJ-6aeFlVMFOtu6kJDKPxwTMe7ZJnmmIkRXMNWFEGYYGq8NlCAbNhKFyGulewwR4fTOUBHQBiQDI0dEdGr0ZJP2jrcZbc10tC1447QVz6_ZVvrhVUx5n-lgiJJVXzeCOZ-6vl-bx6VFTc10EYES77izWOBFVPPlHLBqzSdlysIuI93NkD8E_G4I-HwZg0EpyNtwvLbO4TvKg0137MivLsXAZkuJTY-am7YdxPIonKE3oUFJDeblwytpcKdrOrio7MJX3S3xjSQOA-7Oo4DIYbpVrrldmcLJNWe8x_Syu0HnwnbLJlaS_76DMzUyCQ/http%3A%2F%2Fwww.jeiglesias.com%C2%A0From%3A%C2%A0freesurfer-bounces%40nmr.mgh.harvard.edu
  on behalf of Corinne Alison 
Donnay Date: Wednesday, April 10, 
2024 at 8:39 AMTo: Freesurfer support list 
Subject: Re: [Freesurfer] 
WMH-SynthSeg - Torch module not 
foundExternal Email - Use 
CautionHi 
Eugenio,  Thanks for getting back to me – I had the newest version 
installed and still get the same error (pasted below). mri_WMHsynthseg --i 
flair_ax.nii.gz --o flair_ax_WML.nii.gz --threads -1 Arguments seem 
correct; loading Python packages...Traceback (most recent call last):  
File 
"/usr/local/apps/freesurfer/dev-2024-04-19/python/packages/WMHSynthSeg/inference.py",
 line 284, in     main()  File 
"/usr/local/apps/freesurfer/dev-2024-04-19/python/packages/WMHSynthSeg/inference.py",
 line 76, in main    import torchModuleNotFoundError: No module named 
'torch' I also installed FreeSurfer 7.4.1. Would you be able to expand on 
what you mean by  “a way around this is installing FreeSurfer 7.4.1, and 
using its fspython to run the WMh-SynthSeg code”? I loaded FreeSurfer 
7.4.1, and then changed the location of the model in inference.py and tried 
using FreeSurfer 7.4.1 fspython but now its missing the 'unet3d' 
module: [donnayca@cn4270 anat]$ module load freesurfer[-] Unloading 
freesurfer  7.4.1 on cn4270 [+] Loading freesurfer  7.4.1  
on cn4270  [donnayca@cn4270 anat]$ fspython ../inference_cd.py --i 
flair_ax.nii.gz --o flair_ax_WML.nii.gzArguments seem correct; loading Python 
packages...Traceback (most recent call last):  File "../inference_cd.py", 
line 285, in     main()  File 
"../inference_cd.py", line 79, in main    from unet3d.model import 
UNet3DModuleNotFoundError: No module named 'unet3d'[donnayca@cn4270 anat]$ 
fspythonPython 3.8.13 (default, Apr 21 2022, 14:55:37) [GCC 8.3.1 20190311 
(Red Hat 8.3.1-3)] on linuxType "help", "copyright", "credits" or "license" for 
more information.>>> exit() Thank 
you!CorinneFrom:  on behalf 
of "Iglesias Gonzalez, Juan E." 
Reply-To: Freesurfer support list 
Date: Saturday, April 6, 2024 at 
1:04 PMTo: Freesurfer support list 
Subject: Re: [Freesurfer] 
WMH-SynthSeg - Torch module not found Wrong answer: apparently this has 
been fixed in the latest dev; maybe try that?Cheers,/Eugenio --Juan 
Eugenio 
Iglesiashttp://http://secure-web.cisco.com/1Bz_4nONhypuVg0at2yxM7j3iTzJ-6aeFlVMFOtu6kJDKPxwTMe7ZJnmmIkRXMNWFEGYYGq8NlCAbNhKFyGulewwR4fTOUBHQBiQDI0dEdGr0ZJP2jrcZbc10tC1447QVz6_ZVvrhVUx5n-lgiJJVXzeCOZ-6vl-bx6VFTc10EYES77izWOBFVPPlHLBqzSdlysIuI93NkD8E_G4I-HwZg0EpyNtwvLbO4TvKg0137MivLsXAZkuJTY-am7YdxPIonKE3oUFJDeblwytpcKdrOrio7MJX3S3xjSQOA-7Oo4DIYbpVrrldmcLJNWe8x_Syu0HnwnbLJlaS_76DMzUyCQ/http%3A%2F%2Fwww.jeiglesias.com%C2%A0From%3A%C2%A0freesurfer-bounces%40nmr.mgh.harvard.edu
  on behalf of Iglesias Gonzalez, 
Juan E. Date: Friday, April 5, 
2024 at 3:58 PMTo: Freesurfer support list 
Subject: Re: [Freesurfer] 
WMH-SynthSeg - Torch module not foundDear Corinne,A bunch of libraries are 
currently broken in the development version; apologies for this. A way around 
this is installing FreeSurfer 7.4.1, and using its fspython to run the 
WMh-SynthSeg code. Apologies for the inconvenience!Cheers,/EPS: I just updated 
the wiki to include this information. --Juan Eugenio 
Iglesiashttp://http://secure-web.cisco.com/1Bz_4nONhypuVg0at2yxM7j3iTzJ-6aeFlVMFOtu6kJDKPxwT

Re: [Freesurfer] Question about mris_compute_lgi error: /scratch/tp94c480ef_a005_4f9a_85af_ab56b34400cd.load_mgh.m.mgh: Permission denied")

2024-04-03 Thread fsbuild

External Email - Use Caution

 The permissions on /scratch may not be set to allow you to write files 
there.  If it does not work from the terminal window to create a plain 
file there via the command,
$ touch /scratch/foo
- then you will get the same permission denied error.
If the above fails, then you should contact whoever setup the machine, your IT 
department, etc. and ask them to provide write permission there.
- R,

Begin forwarded message:From: XinRan Wu 
Subject: [Freesurfer] Question about mris_compute_lgi error: 
/scratch/tp94c480ef_a005_4f9a_85af_ab56b34400cd.load_mgh.m.mgh: Permission 
denied")
Date: April 3, 2024 at 12:14:38 EDT
To: freesurfer@nmr.mgh.harvard.edu
Reply-To: Freesurfer support list 

ERROR: could not open /scratch/

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is 
addressed.  If you believe this e-mail was sent to you in error and the e-mail 
contains patient information, please contact the Mass General Brigham 
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline 
 .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail.

Re: [Freesurfer] Support for GPU on Freesurfer

2024-04-03 Thread fsbuild

External Email - Use Caution

Use of parallelization depends upon the order of how the data needs to be
processed. The recon-all command is not single command, but a
wrapper command that runs a sequence or pipeline of many lower level freesurfer
commands in a certain order. It’s not unexpected for recon-all of the
subject bert data to take ~8 hours on a consumer (non-server, non-cluster),
stand-alone machine, e.g. recent Intel I9 chip with 8 physical (performance) ~3
GHz cores, 8 virtual cores, 32G of DDR4 RAM and an SSD drive. If you have
access to a computing cluster, you could try running recon-all there - which
should reduce the processing time.
- R.

On Apr 3, 2024, at 14:58, Camargo, Aldo
wrote:External Email - Use
CautionHi there,I was
wondering if there is support for GPU on FreeSurfer. I really would like
to use it on GPU because is taking 9 hours per subject to recon-all.Thanks a
lot and have a nice day,Aldo CamargoSenior Postdoctoral Fellow at the
University of Maryland,
Baltimore___Freesurfer mailing
listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr..mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] [FreeSurfer] Lesion detection at different thresholds

2024-04-01 Thread fsbuild

External Email - Use Caution

 You can try using the Silicon Mac development build on the M2 
machine..  The download links is,
https://secure-web.cisco.com/1sX8Y1I4GPyZJYzijtfGnav0Xe1MBg-Yv4HzZ07-_su8lv08rzyK4H8-8kXDApCOFJi1XX2mYF4_iH04jySngiX_PsKXZ8K48PCmsO5rOdoTp9xOkS_lWIvP4_shoz9L0juTGXnI-cJu2OkSgIHq0t6kpJ57R6CDFuWwj6oo8ei6KgjsNlR3paBqlrIqqcBQfav6WRebfuIDaklO-u0z1WbqE8x5ZAYkk1eEWo54Lx3BivsKo1mU8doLnUImjSzTlys0yMQMxLZGbQ6ImK6nlKCF1Oetn2F4eojop3JuQT_CvEul9WKC1RN8IawLUeyXxhXl7B8LJ_c2ZifIfLarE6A/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Fpub%2Fdist%2Ffreesurfer%2Fdev%2Ffreesurfer-macOS-darwin_arm64-dev-20240327.pkg
Right click on the pkg installer and then select the “open with installer.app 
…” option.

- R.

On Apr 1, 2024, at 20:40, Martin Juneja  
wrote:External Email - Use 
CautionHi Koen and Doug,I am 
trying to do similar analysis but when I run run_samseg command, it gives me 
error "Illegal Instruction: 4"I am using the FreeSurfer 7.4.1 version on Apple 
M2 Max MacBook Pro 14.4.1.Is it because run_samseg is incompatible with Apple 
M2? If so, could you please suggest any solution (if available) how I can run 
run_samseg on my Apple M2 computer?Thanks.
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is 
addressed.  If you believe this e-mail was sent to you in error and the e-mail 
contains patient information, please contact the Mass General Brigham 
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline 
 .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail.

Re: [Freesurfer] Mac OS Monterrey and XQuartz 2.8.2

2024-03-21 Thread fsbuild

External Email - Use Caution

I would try downloading an installing the latest version of Xquartz which is 
2.8.5 
from,https://secure-web.cisco.com/1QbY1_LKpOs8rxg9YmC2vjno1Z4v2i9V4XhLfDJzwmqCqCNtKYV5iKJ97aqCHBWhugUhe9IammuJUWqdIs7TNqvfslqQ7-iNicm1kKFw4SdTFJkeKTstQV2uZgF4LkFiKVqH_sXmfx4-EyPNQaC-IQhbg6vzxSrPPX9tOITRWcrJAOMPi1YGa5Dl09v7xbqRK9OUZ9YQ44l5cfCBcqoEVYtS3E_ktAaWhBM4NFOXOZuv9n-8Q3grR9r0qor3mFFQR4iL_agscdQM2Ia1iey1d6gjN6-c2SbHRikXbWdVZIp0yC3bWj7QD_htWCal6UddDd-B1CQUGn8Fct_OewW2hRA/https%3A%2F%2Fwww.xquartz.org%2F
Works fine with Monterey (at least on an Intel Mac).
- R.


On Mar 21, 2024, at 19:05, Hugo Sandoval  
wrote:External Email - Use 
CautionHi, i am trying to 
install freesurfer using Mac OS Monterrey and XQuartz 2.8.2.  I get 
an error message.  Is it not 
compatible?___Freesurfer mailing 
listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is 
addressed.  If you believe this e-mail was sent to you in error and the e-mail 
contains patient information, please contact the Mass General Brigham 
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline 
 .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail.

Re: [Freesurfer] Bug reporting - longmc: case-sensitive issue in variable

2024-03-19 Thread fsbuild

External Email - Use Caution

 On Ubuntu linux the default shell may still be “dash” and not the “bash” 
shell.  Dash cannot parse all bash scripting, so type “bash” or try 
setting “bash” to be your default shell and then run commands.
- R.

On Mar 19, 2024, at 22:17, Boscutti, Andrea  
wrote:External Email - Use 
CautionHello FreeSurfer 
Developers,When attempting to run "recon-all -long" in subjects with multiple 
T1 inputs, I get the following error when "longmc" is run:concatLtas: Undefined 
variable.if: Expression Syntax.Command exited with non-zero status 1For the 
entire log, see attached "longmc_error.log".The following change at line 188 of 
"freesurfer/bin/longmc" fixes it (case-sensitive issue in "$concatLtas"):set ud 
= `UpdateNeeded $origvol $CrossList $concatLtas  -->  set ud = 
`UpdateNeeded $origvol $CrossList 
$ConcatLtas`Best,Andrea___Freesurfer
 mailing 
listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is 
addressed.  If you believe this e-mail was sent to you in error and the e-mail 
contains patient information, please contact the Mass General Brigham 
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline 
 .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail.

[Freesurfer] mri_synthseg fails with current model files (was Re: Support Request NextBrain)

2024-02-28 Thread fsbuild

External Email - Use Caution

I don’t believe the workaround will be supported or provided with future 
releases intended to run on Silicon Macs.  If there is still an issue with 
mri_synthseg running with the current model files in the freesurfer dev build, 
then please let us know the details.
- R.

On Feb 28, 2024, at 20:11, Sorby-Adams, Annabel 
<asorby-ad...@mgh.harvard.edu> wrote:Hi Helen,I managed to run 
mri_synthseg on my M2 Mac by coping over the model file to the 7.3.2 version of 
freesurfer, and installing the tensorflow workaround previously posted on the 
forum for apple silicon machines.I have not been able to get it to work on the 
7.4 or most recent dev versions unfortunately. The work around for 7.3.2 isn’t 
ideal, but does the trick. Freesurfer gurus may have more insight 
though! AnnabelOn 28 Feb 2024, at 20:03, Friedrich, Helen 
<hfriedr...@bwh.harvard.edu> wrote:Hi R,Thanks for your quick 
response. We actually did that initially and it did not work 
unfortunately.Could you provide me with segmentations for a certain scan? Or do 
you see any other possibility to make it 
work? Best,Helen__ Helen Friedrich, B.Sc.Doctoral 
Student Netstim Laboratory Center for Brain Circuit 
TherapeuticsDepartment of Neurology Harvard Medical SchoolBrigham and 
Women’s Hospital 75 Francis St, Boston MA 
02115 brighamandwomens.org   <Outlook-rrf3zs4o.png> Von: fsbuild
 <fsbu...@contbay.com>Gesendet: Mittwoch, 28. Februar 2024 
17:20An: freesurfer@nmr.mgh.harvard.edu 
<freesurfer@nmr.mgh.harvard.edu>Cc: Friedrich, Helen 
<hfriedr...@bwh.harvard.edu>Betreff: Re: [Freesurfer] Support 
Request NextBrain External 
Email - Use Caution The 
mri_synthseg script and python in the freesurfer disrtibution you are running 
are not entirely compatible with the arm64 M1, M2, M3 processors in silicon 
Macs.   You could try installing and running the development build of 
Freesurfer for the silicon Mac via the link below.  (After download, right 
click on the .pkg installer, and select open with default, then follow the 
prompts).https://secure-web.cisco.com/1lFsgk7vtXlatyZGhw2wfTf_WTyioo4BmLzbKYJKS0chTLAdh3oNub0eu9G9qOzY1R1TPfh7O0cjIMQFuYhTlqUAiRdSgB91d0F3QHYByNFAVNjpsEEv4j8KUjqvzZLZqXEgP3pCVveZdU3qRAuGidK7qzpvBYz_YCjvjuBw1oBU1uPE747lnnMIYvx8VMwRVlcOMe3jWSxtNYLK8z_NDUA_K1a4C_SuFXhsDf1Div6UKtS7i7jpzOLjru_-tpPY3gKSfhG_l5s6JEbjagAkRoXdEm1sYZTLvjnL5yV99Wpxmx2NKrzlsvr_ucGSkEhwaNz9EMh0iPkmf8X102ExqfA/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Fpub%2Fdist%2Ffreesurfer%2Fdev%2Ffreesurfer-macOS-darwin_arm64-dev.pkgWe
 would be interested to know if you run into such issues with the above 
development build.  Please keep in mind a development build can be 
unstable and has not been tested like an actual release.  Your numerical 
result may differ with the development build compared to the previous 
build/release.- R.On Feb 28, 2024, at 14:25, Friedrich, Helen 
<hfriedr...@bwh.harvard.edu> wrote:Dear Support Team,I'm reaching out for 
assistance with setting up NextBrain - mri_synthseg. Unfortunately, I 
could not make it work. There seems to be an issue with the 
np.float128-section. This error keeps showing up: <image.png>I have 
also tried to delete np.float128 from the script (as per suggestion from my 
colleague). However, the same error showed up. I'm working on a macOS 
M1. I would be very grateful for your 
assistance. Best, Helen __ Helen 
Friedrich, B.Sc.Doctoral Student Netstim Laboratory Center for Brain 
Circuit TherapeuticsDepartment of Neurology Harvard Medical SchoolBrigham 
and Women’s Hospital 75 Francis St, Boston MA 02115 MailScanner has 
detected a possible fraud attempt from "secure-web.cisco.com" claiming to 
be brighamandwomens.org   <Outlook-jaw0jfh4.png> ___Freesurfer
 mailing listfreesur...@nmr.mgh.harvard.eduMailScanner has detected a possible 
fraud attempt from "secure-web.cisco.com" claiming to 
be https://secure-web.cisco.com/1rwDcenDHH042rGVnR9ADpR-TvoThnsOLxqL-WqiCsQXlodLvLH8LTsAf1UlTVWuEp53n7GP9_RUeZ2zg9Z2OjiIkAzj4i1I3r7BWZ9yej6K3qLG_Fsr4ngpe8HgSP3aG_ovKSBkDEN-4oG3T8odCmFHoLy5fQaV_FCeJ1Oms-2XscpGn-wph0VpO91I61dgtvQpUHXYPSYkE8xxZo25dN1JzjOsLlaCpcbhu0KQgwjSBkZ18Pd6mrnXirX80G6Q6O9hG_MHBJ2n3e0ZiAezwii6YRX9py4kmNFAm6usGa9jgoXWPQHlHQpqSSbkOh6zhMjDmNezK_QKtCp908UKk7g/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer___Freesurfer
 mailing 
listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer<Outlook-rrf3zs4o.png>___Freesurfer
 mailing 
listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr..mgh.harvard.edu/mailman/listinfo/freesurfer

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.m

Re: [Freesurfer] Support Request NextBrain

2024-02-28 Thread fsbuild

External Email - Use Caution

The mri_synthseg script and python in the freesurfer disrtibution you are
running are not entirely compatible with the arm64 M1, M2, M3 processors in
silicon Macs. You could try installing and running the development build
of Freesurfer for the silicon Mac via the link below. (After download,
right click on the .pkg installer, and select open with default, then follow
the prompts).
https://secure-web.cisco.com/1lATTVPHpR_oCFmftTB7zqKpLVwajHCxZOKmxSn1tiCG2YsAguxO-onjfRFFoIAelBuq4VwcqflHZjVdKsNn_DE-IM537PyttVIVTZWBlmPHAOh6E6aox44M20RF1jIcKx-xJ1eCPhC9LpLjlB6V67UnFHLwxveDI7e1JBdPwIAbo---1k4E5Vd2QlLAc5xoVz7FNJa-WbB08QJI5kmBVhydQXQClQzGSK4_II7tzn_4XlAiNzRSotGH9cQ_HqzqOo_WfwfMmjdFzYPlYrggTgEyf2t9-LW9-TjBC_y1WWsJo0hegy1WIhcQ7jhakR2SkdHVF-pCrQesnLvB5CVGIfg/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Fpub%2Fdist%2Ffreesurfer%2Fdev%2Ffreesurfer-macOS-darwin_arm64-dev.pkg
We would be interested to know if you run into such issues with the above
development build. Please keep in mind a development build can be
unstable and has not been tested like an actual release. Your numerical
result may differ with the development build compared to the previous
build/release.
- R.

On Feb 28, 2024, at 14:25, Friedrich, Helen
wrote:Dear Support Team,I'm reaching out for assistance with setting up
NextBrain - mri_synthseg. Unfortunately, I could not make it work. There
seems to be an issue with the np.float128-section. This error keeps showing
up: I have also tried to delete np.float128 from the
script (as per suggestion from my colleague). However, the same error showed
up. I'm working on a macOS M1. I would be very grateful for your
assistance. Best, Helen __ Helen
Friedrich, B.Sc.Doctoral Student Netstim Laboratory Center for Brain
Circuit TherapeuticsDepartment of Neurology Harvard Medical SchoolBrigham
and Women’s Hospital 75 Francis St, Boston MA
02115 brighamandwomens.org ___Freesurfer
mailing
listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] Updated instructions for running Freesurfer in a Linux VM (virtual machine)

2024-02-26 Thread fsbuild

External Email - Use Caution

 Instructions about how to setup a VM running Ubuntu 22.04 LTS Linux have 
been updated on the wiki page,
  
 https://secure-web.cisco.com/1-hfMzPT3UMB77kyvVjV7UDTVoojwvFmLCgo5iFkfwXwZ25LXFS9Roz8W9yuwq3ZMgs5tjQSEKQlcqIQbRxJ1rps2AabjEIivAzU8ekg5AsJLT6mntG2Nc4NnzZYDPJZG2wf_aLnz6uKLNaustProbSHYKiMbskeae7cLki3u_nSnw4xu4chaYhm-Z5kLiuCwcqECsDkdCMoITT-JKqqCHPkmz-brMCz3F9oCcmaqFMirOwqvqcbah9n7ycsFnHd3RDgkGDoMo6zuiX8aecB8B0MO5X6QvJKUslOgGjkBUQ4W4ItrfjjElVnPeg2YV9CgmgVdxPZUx-arGQMnQ7ZyPg/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FVM_67The
 instructions include how to install and run the current Freesurfer release 
(7.4.1 from June 2023).
Please keep in mind that while the VirtualBox virtualization application runs 
on hosts with Intel processors, it does not run on arm64 machines (including 
silicon Macs with M1, M2, M3 chips).
- R.
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is 
addressed.  If you believe this e-mail was sent to you in error and the e-mail 
contains patient information, please contact the Mass General Brigham 
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline 
 .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail.

[Freesurfer] 7.4.1 release archive has extra directory prepended

2024-02-25 Thread fsbuild

External Email - Use Caution

 The leading ./ in the path looks like a by-product of needing to use 
various/different options now in creating the tar archives and also the tar 
command running may be from a different system.  Not sure that can be 
reverted.
- R.Hi Freesurfer, Wasn’t sure where to post this as the github is more 
for source code issues.The 7.4.1 archives all have ‘./’ prepended to them 
(i.e., ‘./freesurfer/’ vs ‘freesurfer/’). This is causing an issue with 
neurodocker as the definition file it creates  strips the first directory 
when building images. Thus, containers built on the 7.4.1 archives need to have 
their paths changed compared to prior versions or they need to strip the first 
2 levels of the path. It’s not a big deal and easy to fix in the def files 
once it's figured out, but given that it’s a departure from prior releases and 
is breaking some of the downstream tools, perhaps the next releases can go back 
to just 1 level deep (i.e. ‘freesurfer’)?  Cheers,Dylan 
Wagner
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is 
addressed.  If you believe this e-mail was sent to you in error and the e-mail 
contains patient information, please contact the Mass General Brigham 
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline 
 .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail.

Re: [Freesurfer] recon-all-clinical synthseg error

2024-02-25 Thread fsbuild

External Email - Use Caution

 It could help to know what OS version and what Freesurfer version you are 
running.  From your path /usr/local/freesurfer it looks like you are 
running a Freesurfer release, e.g., 7.4.1.
- R.

On Feb 25, 2024, at 21:45, Agata Wolna  
wrote:External Email - Use 
CautionHi!I'm trying to run 
recon-all-clinical but I'm running into an error with the SynthSeg at the very 
beginning. Do you have any hints what the problem might be here? Here's the 
full error message:the following problem occured with 
image [mypath]/mri/native.mgz :Traceback (most recent call last):  
File "/usr/local/freesurfer/python/scripts/mri_synthseg", line 303, in 
predict    image, aff, h, im_res, shape, pad_idx, crop_idx = 
preprocess(path_image=path_images[i],  File 
"/usr/local/freesurfer/python/scripts/mri_synthseg", line 554, in 
preprocess    im, _, aff, n_dims, n_channels, h, im_res = 
get_volume_info(path_image, True)  File 
"/usr/local/freesurfer/python/scripts/mri_synthseg", line 1456, in 
get_volume_info    im, aff, header = load_volume(path_volume, 
im_only=False)  File "/usr/local/freesurfer/python/scripts/mri_synthseg", 
line 1377, in load_volume    x = nib.load(path_volume)  File 
"/usr/local/freesurfer/python/lib/python3..8/site-packages/nibabel/loadsave.py",
 line 110, in load    img = image_klass.from_filename(filename, 
**kwargs)  File 
"/usr/local/freesurfer/python/lib/python3.8/site-packages/nibabel/dataobj_images.py",
 line 503, in from_filename    return klass.from_file_map(file_map, 
mmap=mmap, keep_file_open=keep_file_open)  File 
"/usr/local/freesurfer/python/lib/python3.8/site-packages/nibabel/freesurfer/mghformat.py",
 line 526, in from_file_map    header = 
klass.header_class.from_fileobj(mghf)  File 
"/usr/local/freesurfer/python/lib/python3.8/site-packages/nibabel/freesurfer/mghformat.py",
 line 171, in from_fileobj    + 
int(klass._data_type_codes.bytespervox[tp]) * 
np.prod(hdr_str_to_np['dims'])KeyError: 10resuming program executionERROR: some 
problems occured for the following inputs (see corresponding errors 
above):[mypath]/mri/native.mgzError in 
SynthSegBest,Agata___Freesurfer 
mailing 
listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is 
addressed.  If you believe this e-mail was sent to you in error and the e-mail 
contains patient information, please contact the Mass General Brigham 
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline 
 .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail.

Re: [Freesurfer] Mac OS M2 M3 computers

2024-02-17 Thread fsbuild

External Email - Use Caution

If you don’t have a license.txt file setup to read, then freeview will not run.
If you have not already done so, I would set the environment variable 
FS_LICENSE to point to the license.txt file you downloaded after registering, 
e.g., if license.txt is in your home directory and your user name is “cstevens” 
then
$ export FS_LICENSE=/Users/cstevens/license.txt$ head -1 
$fs_license...@somewhere.com  <——  email you used to register
You can put that define in your shell initialization file so you do not have to 
set it again when you login.
If you are doing long term work, we recommend you download and install the 
7.4.1 release from June 2023.  Those are Intel binaries, but they should 
run.  You should use the standard Mac .pkg file.  Right click on the 
.pkg file icon, select open with installer.app (default) which should provide 
some security exemptions.
June 2023 7.4.1 
releasehttps://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/7.4.1/freesurfer-macOS-darwin_x86_64-7.4.1.pkg
There is a native Silicon Mac development build, but it is unstable and has not 
been tested as a full release has been.  But if you are only running 
freeview, then you could try that instead..  Install the same way as 
listed above by right clicking.
Development 
buildhttps://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev/freesurfer-macOS-darwin_arm64-dev.pkg
- R.

On Feb 17, 2024, at 22:09, Charles Leger 
 
wrote:   External Email - Use Caution 
   Really. I have a Mac Mini M2 (16GB), 
8 cores. I downloaded FreeSurferMac OS 7.4.1. Then tried freeview and loaded a 
T1 image. Freeviewimmediately closed. I tried this 3 times with the same 
result. PerhapsI should try a different version, ideally a version that allows 
CPUrather than a GPU install.Best,COn Sun, Feb 4, 2024 at 12:50 AM Fatima Karim 
 
wrote:   External Email - Use CautionI 
have been using free surfer for a year nowon Mac m2 max and it's working 
fine.On Sat, Feb 3, 2024, 23:42 Charles Leger 
 
wrote:   External Email - Use 
CautionThere seems to be some contention if FreeSurfer will support Mac 
OSsilicon (M2, M3) computers. In the technical requirements section, itis 
clearly specified that a " 3D graphics card with its own graphicsmemory & 
accelerated OpenGL drivers" is required. But in the emailarchive (caution 
suggested) it is noted that "binaries should run oncurrent Macs with M1, M2, M3 
arm64".Currently. Apple has not indicated plans to support eGPUs, which, 
onpaper, makes all newer non-intel Mac computers not compatible 
withFreeSurfer.Any suggestions would be greatly 
appreciated.--*Dr. Charles Stevens 
LegerPhD Psychology, Neuroscience diplomaDepartment of PsychologyConcordia 
University7141 Sherbrooke Street W.Montreal, Quebec, CanadaH4B 
1R6___Freesurfer mailing 
listfreesur...@nmr.mgh.harvard.eduMailScanner has detected a possible fraud 
attempt from "secure-web.cisco.com" claiming to be 
https://secure-web.cisco.com/1swIjR2PdKJ-tGWCqLlTzXXnPbNpDqwl7lVLV9r_aC1CVBUJA9_RbBE2kgRn27WfUcfa0ggUCmkIDbEh5doMeoCe1P1Mk7ghtCPlKlYtnO5Zpt_AMCNWKbCAq1gO2xF3do-4bLQlHAPuH1lO4gThEIdMNph7vL60Q-8JTr6lHaTmsQ_Bxmay7wliyd9s6gDjjdsCgkpZ-GCqgn4lrHXwblfrqSuxp5cQcUlTFTtTKKd4TN-pSA2mgucdW5BUqJPL85hZQD0PRkI4ma_5IQl8LvhmTx35KbeRK_BGGAZ79hBFzJUDa7uPFA00JL3JU0yR9ZcqQjDMwXSK5VhCeaHlbxA/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2FfreesurferThe
 information in this e-mail is intended only for the person to whom it is 
addressed.  If you believe this e-mail was sent to you in error and the 
e-mail contains patient information, please contact the Mass General Brigham 
Compliance HelpLine at MailScanner has detected a possible fraud attempt from 
"secure-web.cisco.com" claiming to be 
https://secure-web.cisco.com/1Wm-LbShKwZnggMKu70mgCrqBikmdTG-n5C_oMDoGIo-ejXMLmE2pFp7238dDpRA2syCMdftPNjnUOrYcZ8cmnRIzfpzY_rE_wLEOfKpAAGG1l6kX9P6Dprr429zr_W2w1jOtkms_ju5oFqQvNqNqbdCyxwlPkLCXzOvVwmHi95JNqQvnKgIq0WEi-fDv43ynu7kong2lixS68Lo2a-ypmZ-dpbIpC6Ozqc0AbWK9WdfEX-Mhbl_c3UKyYPwy7bq_1mntvGjp7ODhT48aZslEosjaesH_uTF8iLKWhDmCvmzkkmVE3mm_Qmk7DJd0kHimGOuTb5LZmggNpsh-GiyTUQ/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline
 ;
 .___Freesurfer mailing 
listfreesur...@nmr.mgh.harvar

Re: [Freesurfer] mpr2mni305 failed

2024-02-09 Thread fsbuild

External Email - Use Caution

 The recon-all log contains this entry,
ERROR: mpr2mni305 failed, see transforms/talairach_avi.log
If you go to where that log file is, which I think would be,
$ cd $SUBJECTS_DIR/mri/transforms
… then look in that log file to see what the error is.  It is usually at 
the end of the log file.
- R.

On Feb 9, 2024, at 07:16, Francesco Lomi  
wrote:External Email - Use 
CautionUnfortunately I've tried 
to change the directory but I've encountered the same error, as shown in the 
log file. Best,FrancescoIl giorno gio 8 feb 2024 alle ore 17:59 Huang, 
Yujing  ha scritto:This is from your 
recon-all.log: “setenv SUBJECTS_DIR 
/home/ubuntu/freesurfer/subjectsFREESURFER_HOME /home/ubuntu/freesurferActual 
FREESURFER_HOME /home/ubuntu/Freesurfer“Your SUBJECTS_DIR points to your 
Freesurfer install directory - /home/ubuntu/freesurfer/subjects. I’m not sure 
if this is the reason for the failure. But it is a good idea to set 
SUBJECTS_DIR to some other directory where you have write permissions. Can 
you re-set SUBJECTS_DIR and try 
again? Best, Yujing   From: freesurfer-boun...@nmr.mgh.harvard.edu  On
 Behalf Of Francesco LomiSent: Thursday, February 8, 2024 11:44 
AMTo: Freesurfer support list 
Subject: Re: [Freesurfer] mpr2mni305 
failed External Email - 
Use CautionYes, sure. This is 
the fileThanks.  Il giorno gio 8 feb 2024 alle ore 17:03 Huang, 
Yujing  ha scritto:Can you re-send 
recon-all.log as 
attachment? From: freesurfer-boun...@nmr.mgh.harvard.edu  On
 Behalf Of Francesco LomiSent: Thursday, February 8, 2024 10:58 
AMTo: freesur...@nmr.mgh.harvard.eduSubject: [Freesurfer] mpr2mni305 
failed External Email - 
Use CautionHello 
everybody, I'm new on Freesurfer and I've installed the software on 
my Ubuntu 20.04 machine. The installation should be fine. just tried to run 
recon-all on my subject data but i got stuck on the following error you can see 
on the screenshot:  Any idea on how to fix 
this?Thank you in 
advance Best,Francesco___Freesurfer
 mailing listfreesur...@nmr.mgh.harvard.eduMailScanner has detected a possible 
fraud attempt from "secure-web.cisco.com" claiming to 
be https://secure-web.cisco.com/1XbsZgwTnI3onjdYJVFjoCKwtbD8UOXL2chYPXyZAPt9Lp3eMX9vyw40TUvskG4dYYkm2a_i5GuY1eCxRlu-mfonDPnSeXcAzNR-GZPnBfEVQZHquR8lKVpFOlFewKsO_X2LVEZNCFWF2GvofOcyDZCHKuaau8ii59MRzU16AracbZCydu2OzREp9Fzga1x-4s4FugvWLSJT13nsCDuxyFhJjI6XiLDfvpQDezEvUs8cAGdlxwbF1OgwxW_uWZj0t7n8645RpoR0dYGaE3em4IsiK8xd21K-syRY3hmKMpr7mh1-sHn8OiLAzzqaS6Pngsj_1Swi77LJ2rlwsn3gqoQ/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2FfreesurferThe
 information in this e-mail is intended only for the person to whom it is 
addressed.  If you believe this e-mail was sent to you in error and the 
e-mail contains patient information, please contact the Mass General Brigham 
Compliance HelpLine at MailScanner has detected a possible fraud attempt 
from "secure-web.cisco.com" claiming to 
be https://secure-web.cisco.com/1AWr9-RI-XVYXogeF7gwubnfYP8OHUBQfXOW1xkbCfUaChH1R4IH5fZI2v1ZYLsdFTDE0fR9uKUOHlAXQvkG_kNzEx0Gc5ZoNFEaMhFlkWl7FB4tfo6IFOvN56vC7FR0n5K3UjPdQV9vnwNYr7SUmrg9nYPhjInMJc8QZGtcWfw7yk4hAzFzaN9Ut91RYTZtfObHnna7oGsJYpHcvhrYIu8QVaXe04I6qR8LfNCmP2oehk6feF0ybTM8Y3TuxPffP9OefcorJGniJpuKjmO6pg4Y34aiQPYMKku7rILafn1eqgju48ysr0FCBsj21oJbBtPDvpOSsiFkVVmmGtPLLxw/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline%26nbsp;

Re: [Freesurfer] Synthsr command !

2024-02-08 Thread fsbuild

External Email - Use Caution

The python distribution in the 7.4.1 release cannot run all the python based 
tools on a Silicon Mac (M1, M2, M3 chip) because at that time we did not have a 
python distribution that was completely compatible with the arm64 architecture.
We currently have a development build for the Silicon Mac, and you can 
download/try the installer package from:
https://secure-web.cisco.com/1iKFStD8SwFv0R2HIbwHmO8r1CRu1iDcQPEOYPG7jJvIjrAZDc0sJfHDQhWwcyZciKr78g2onoB2sSzz0vQI9hVrgYAlB6is6icLuMg76sWtQfUyNgcNnd1Q1wRYOF1dtT7BTdoIZesFyDrdB8pc3sSifAM_h9enQbvhLW4Fpsq9yGMR8UFc_k8RJbm43sAox64SI8W4Kj6foRBXU_6oeiy43-jspvGAXGRjGJEUNvS2ySV30aGfFwbfZpwL4oaHGelrKhzER-r6Eb1-Ikus3WmL6dTNPOYDZFhvhpZQoiknNDp1rGQyDXPL5soFZag0R2QFjbjrBsXSdTFdZ5ECtAA/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Fpub%2Fdist%2Ffreesurfer%2Fdev%2Ffreesurfer-macOS-darwin_arm64-dev.pkg
But we cannot recommend this build for ongoing work as it is currently unstable 
and not a tested release.
- R.

On Feb 7, 2024, at 17:05, Martin Juneja  
wrote:External Email - Use 
CautionDear Juan and FreeSurfer 
developers,I am trying to run the mri_synthsr command on a MacPro M2 
Max chip (OS 13.6.4) - but somehow, I am getting the following error when 
I try to run this command. I am using FreeSurfer's 7.4.1 version.Illegal 
instruction: 4I would greatly appreciate any help in getting this 
resolved.Thanks.___Freesurfer 
mailing 
listfreesur...@nmr.mgh..harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is 
addressed.  If you believe this e-mail was sent to you in error and the e-mail 
contains patient information, please contact the Mass General Brigham 
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline 
 .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail.

Re: [Freesurfer] Help Download FreeSurfer Windows VM

2024-02-06 Thread fsbuild

External Email - Use Caution

We don’t expect things to work reliably with 8G total RAM for the machine. 
 The host machine itself will always consume some memory when running its 
OS, probably up to a few Gig, leaving even  less than 8G to be used for 
running the VM with freesurfer.
The Virtualbox VM is no longer available because the security/login credentials 
were compromised on this list.
Since you are on Windows, you could try using the windows OS built in Windows 
Subsystem for Linux (WSL).  We have some notes about setting that up at,
https://secure-web.cisco.com/15CztkRxVJ7Ddir4MS_9Arksy0DkD_t2mgoGcHYmhJKK5Lsyhn9OQQF2n11zmSLeqbeGjffl8JiKJspStS5BIEqDeW4hwjubpORcz_WfM_QelzOOGCbo0-yxIrw5CRp9OTe6G_opwaoTix1AU6qWdzQ84fN4r922b3CXNohHY0nfJE_R1L5EMyO6V8j9OBROkgqBF4F3YCyusFxnCekqZ6zfNabw_pTnvaJDgwZR0JLlJ5nw84ZNy4DAJEMie-rQ8TdAxUT8Hafmh1q3BlprlvLyJxQ9QWTHDvp0ztYKxEOP5KBlgWyaJl3eak96w5YgK1ETj64k1_2sTQtEOkUs3sQ/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFS7_wsl
But you would still likely run into the same issues consistent with having less 
than 8G of RAM to run Ubuntu Linux in WSL (instead of VirtualBox) + running 
freesurfer.
- R.
On Feb 6, 2024, at 08:54, lioudadraca...@gmail.com 
wrote:External Email - Use 
CautionHello FreeSurfer 
Developers,I am attempting to start Ubuntu via VirtualBox 7.0 on Windows 10. 
But I have few problems.First, I do not have the access to the compressed VM 
Image file (FS_7_3_2_course_ubuntu_18_04_06.ova.7z), is it still possible to 
have an access to that ? Second, I've seen that it also requires a login 
password for the "Developer" account. Is it possible to also have the password 
?Finally, I have a 8Go RAM, even if a 16Go is recommended, will it be able to 
run Freesurfer ? Thank you for your help.Best 
regards,Liouda___Freesurfer mailing 
listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is 
addressed.  If you believe this e-mail was sent to you in error and the e-mail 
contains patient information, please contact the Mass General Brigham 
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline 
 .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail.

Re: [Freesurfer] Command terminated by signal 11 when execute mris_place_surface

2024-02-05 Thread fsbuild

External Email - Use Caution

I would look for the core file under /var/crash as close to the time to the
command failure and see what it says.
Signal 11 is a segmentation violation meaning invalid memory access. It
could be that a VM on your machine does not have enough memory to run
recon-all. Or I assume the 32G RAM listed below is the total
physical RAM on the machine and the VM has some portion of that assigned to it.
If you did not assign the VM say 16G-24G of RAM out of that 32G total,
then it might be having a memory issue. You could try not running
anything else on the machine, giving the VM 24G and that would leave 8G for the
host machine. You could also try giving the VM 4 out of the 16 CPUs as
well.
- R.
On Feb 6, 2024, at 00:39, Yp Ben
wrote:External Email - Use
CautionHello FreeSurfer
Developers,I'm want to run HCP T1W data of recon-all , but it always failed on
step " WhitePreAparc lh", below is my run information:OS: Ubuntu 22.04.2
LTSMEM: 32GCPU: 16….Command terminated by signal 11...Check the core dump file
under /var/crash...I use 3 different VMs to run the same sample with different
freesurfer versions , 2 are 7.4.1 and another one is 7.2 , but always failed on
this step , I don't know what's the reason cause this failed , can you please
help to have a look ? Thanks a lot
. ___Freesurfer mailing
listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] Mac OS M2 M3 computers

2024-02-04 Thread fsbuild

External Email - Use Caution

 The current 7.4.1 (Intel binary) release from June 2023 should run on 
Silicon Macs and I believe was tested with MacOS (13.X) Ventura.  We did 
not have MacOS (14.X) Sonoma available at that time for testing.  The 
Freeview image viewing application requires graphics/X-Windows and for that you 
need X-Quartz installed on your Mac.  We have a native Silicon Mac 
development build available but it is currently unstable.
The graphics card spec assumed the graphics card has its own dedicated memory. 
 That spec is somewhat obsolete now w.r.t Silicon Macs since their unified 
memory design means the CPU’s and GPU’s share the same memory.  The spec 
to look for on Silicon Macs is how large is “unified memory”.

Commands that are python scripts (and not Intel or arm64 binaries) using 
modules like tensorflow may not work on Silicon Macs when trying to utilize the 
GPU’s.
If you have not already done so, download and install Xquartz,
https://secure-web.cisco.com/1m9nMZoww5EBHuzCVnK1bRHfdp34oRBsReQGIi-7nF_TereiKLeFE0wV4a4heu4IG4aeHTF9KbcxR24tjHn5fIxKqu4LxSEgeQ8wmm8Q4xbnMFHYwYTY0UHlIENTkDMLYo3DlkhFLMAJZlTu1ccE2K1eh3bvTZ-BkbC_tkl75_agj_kbF0KP5y5mHFYc7xQ90ySlgwcCg6IxgC2KaW4OLOMa901CPYe7bgKc-5NLbXuiMNAnf1vaEneXx-ScWAKTyGvJMmrMqc3PZ63Q0MH6U7ctsM465JxdY4JDmrLuiw_fYKbwEs5j8SKmg_4OFKIOugXUUbkp4dpWCQFQXYurT1Q/https%3A%2F%2Fwww.xquartz.org
The 7.4.1 installer package can be downloaded from,
https://secure-web.cisco.com/1sijobmA3UkgB0Ha5oTzDO0KSCYb2unjOllCiEFgnLqS_Tx2LDrErGMRSS2lvZUAYzU2QZ1ZTncLzfdGcfuepyVFU3QiOnQAOTCWeUaRJ1_tKS4Rte9Ip5fLBZKhbmlE0tznV3WiY2-QKfEKo2T9KPiLpeHSMHVTvZzLeYaEJVWbOk9ABy_rNH35nm3v86C9_eSRlboHzCS_Fjnz9veMWwRi5vCt0T8FtGn94DuzeQQdrq7nDOO96TLwCG2HCkk3TnYzKii68VhahsXqUmxMeF0b9KTHkPngM5SNUX1lC9jHaETzq6i8oLShzbV-OGdZMCjWlRSxqCQgURNIy1wpDFw/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Fpub%2Fdist%2Ffreesurfer%2F7.4.1%2Ffreesurfer-macOS-darwin_x86_64-7.4.1.pkg
RIGHT CLICK on the installer package and under “install with” select the 
default installer.app.  This should bypass having to open system 
preferences to make a security exemption.
- R.

On Feb 4, 2024, at 00:49, Fatima Karim  
wrote:External Email - Use 
CautionI have been using free 
surfer for a year nowon Mac m2 max and it's working fine. On Sat, Feb 3, 
2024, 23:42 Charles Leger  wrote:  
      External Email - Use Caution      
  There seems to be some contention if FreeSurfer will support Mac 
OSsilicon (M2, M3) computers. In the technical requirements section, itis 
clearly specified that a " 3D graphics card with its own graphicsmemory & 
accelerated OpenGL drivers" is required. But in the emailarchive (caution 
suggested) it is noted that "binaries should run oncurrent Macs with M1, M2, M3 
arm64".Currently. Apple has not indicated plans to support eGPUs, which, 
onpaper, makes all newer non-intel Mac computers not compatible 
withFreeSurfer.Any suggestions would be greatly 
appreciated.-- *Dr. Charles 
Stevens LegerPhD Psychology, Neuroscience diplomaDepartment of 
PsychologyConcordia University7141 Sherbrooke Street W.Montreal, Quebec, 
CanadaH4B 1R6___Freesurfer mailing 
listfreesur...@nmr.mgh.harvard.eduMailScanner has detected a possible fraud 
attempt from "secure-web.cisco.com" claiming to 
behttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurferThe information 
in this e-mail is intended only for the person to whom it is addressed.  
If you believe this e-mail was sent to you in error and the e-mail contains 
patient information, please contact the Mass General Brigham Compliance 
HelpLine at MailScanner has detected a possible fraud attempt from 
"secure-web.cisco.com" claiming to 
behttps://http://secure-web.cisco.com/1XhjEdUy0Fa9XN2p8xeFjrDOeCP4-kv91bgNiFttd9lQSt4puwCY-7BT6flcjUAlpSNNTKqS07QyrgvRHSLEkHvIsO_a9YRiODgryd3CXpByugKRyeGXsUiATd_EhjLRnRci3HITDGpeb3JWGirfHAS9eJQgMNB1j2O2Y2fKXhbls2ulwULPKbYbO2fjn_ODWTvOgzlYBCifxq8-Cft-7MjkOHN5HUAPdb_IkoCNpv7uJNIwUb53zqrS2qQDtgR7UImRY36wExU6QNgJJ5sfH34uNveisNOdUuitnuMpatQDqVkGCjhoO-gEc-gKLxPMaS6DMhYJz_IZQri3d16drgg/http%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline%26nbsp;

Re: [Freesurfer] Killed procees during running WMH-SynthSeg

2024-01-30 Thread fsbuild

External Email - Use Caution

 We have seen the (Mac or Linux) OS automatically kill resource greedy 
processes, e.g., commands using large model files.   Increasing the limit 
on physical RAM usage and/or increasing how much data is swapped out to disk 
may still not allow the process to run.  There have been some reports of 
memory leaks in tensorflow/keras python modules, with comments suggesting some 
issues go away when the GPU’s on the machine are no longer used for data 
processing.  I don’t know of a reliable workaround right now. 
- R.

On Jan 30, 2024, at 16:44, Bender, Andrew  
wrote:External Email - Use 
CautionDear Freesurfer 
Experts, I’m evaluating WMH-SynthSeg for white matter lesion segmentation 
using the most recent development version, and ran into similar issues reported 
last month: MailScanner has detected a possible fraud attempt from 
"secure-web.cisco.com" claiming to 
behttps://http://secure-web.cisco.com/1VwtYiRJfeLutN8gPbBz-bZmM0fMIW8vgmy6EkaYe2JAKQ2grPaLmCGo3UpxOnqYUUlcACTvWzy4YIWFwFgTi03QWN8oF6ljo-B1SrjF_YMYXZ8Sa8adrtmKmZC24rjNx1UvnMEKdf7Dr7aNc5Po0duEhAz6rP31ABsIBPEaSU4c8ARZ4bmFR51w452iri2Mpmvl4ZoF6xtPYHmX713youl-9Mdtl3viB5W51pE7xk-HmBcrVYhx8dYvUQPNQSTjEZX9RTAQQrHUJe-RFhDAQHRBvDK9DM9IEqwD3CK3iQRZAb0IOjD2br_bgWkX4uEqz7swGr5atJapDoPcuhXKXMw/http%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg76177.html%26nbsp;I
 was running this as CPU only on a Mac Studio (M2 Ultra) with 192GB RAM. I 
tried is multiple times with 1-8 threads, and the process was killed in each 
instance. Viewing memory usage through the Mac OS Activity Monitor while 
running WMH-Synthseg, it appears that memory usage ramps up to >200GB (at 
which time the process is killed). With system resources consuming ~10GB RAM, 
it seems there should still be sufficient memory if it only requires ~32GB RAM. 
Are there any other (i.e., non-documented) options for running the process on 
CPU only? Any other suggestions are greatly appreciated.. Regardless of 
specific suggestions you may have, I wanted to bring this to your attention as 
a potential bug that could produce memory leaks or similar 
issues. Thanks,Drew   Andrew R. Bender, Ph.D.  
|   Staff Neuroimaging ResearchCleveland Clinic Lou Ruvo Center for 
Brain Health Please consider the environment before printing this 
e-mailCleveland Clinic is a nonprofit, multispecialty academic medical center 
that's recognized in the U.S. and throughout the world for its expertise and 
care. Visit us online at MailScanner has detected a possible fraud attempt 
from "secure-web.cisco.com" claiming to 
be http://secure-web.cisco.com/1wAGnCqYxSltzw75mc2-6ArqL8w0Zro9SfjmjGsOmL-uUNeXPMfZIxlvs9_uOSyk3et2tj48Q9f--hKYxh65e5_ghpQ9qvKWCq_LKkp3AFI9fcrT_e9G4aqDBxmZkUKE0oa5PilsaYVMcaTc4HR6smwk0ccrHw5164PMYnsts8Aeqf51-24ztKvjk5zAn6ZhQ34NCLjIwpyHjuSk1rkcNKVaawoJnX4ecFho-PXt8BtfMX5FlYIQP5XMKDSP3AjZgqpOA97hmc17_zikekqLDemfzqrRzGHeoxUmedsLSdqga4bfylGdKToHzCpwCEeYL9Z7R6Arp4dbVqW438Y_5jQ/http%3A%2F%2Fwww.clevelandclinic.org%26nbsp;for
 a complete listing of our services, staff and locations. Confidentiality Note: 
This message is intended for use only by the individual or entity to which it 
is addressed and may contain information that is privileged, confidential, and 
exempt from disclosure under applicable law. If the reader of this message is 
not the intended recipient or the employee or agent responsible for delivering 
the message to the intended recipient, you are hereby notified that any 
dissemination, distribution or copying of this communication is strictly 
prohibited. If you have received this communication in error, please contact 
the sender immediately and destroy the material in its entirety, whether 
electronic or hard copy. Thank 
you.. ___Freesurfer mailing 
listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is 
addressed.  If you believe this e-mail was sent to you in error and the e-mail 
contains patient information, please contact the Mass General Brigham 
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline 
 .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail.

Re: [Freesurfer] longitudinal hippocampal segmentation error in Mac OS Sonoma + Freesurfer 7.2.0

2024-01-29 Thread fsbuild

External Email - Use Caution

At this point, I think your best bet is to install and run the freesurfer 
7..4.1 release from June 2023 which was tested with R2019b.   Although The 
MathWorks does not support R2019b on MacOS Sonoma, I think we tested the 7.4.1 
release on BigSur, Monterey and Ventura.  So it may work on Sonoma. 
 The 7.2.0 release from 2021 is too old to have been tested on newer 
versions of MacOS.
You can install the 7.4.1 release with the pkg 
installer,https://secure-web.cisco.com/1rsGw8GzmRUK9yxME6fi8OiEwksVSolguqiea92G44m3nZ8vkR_pUdXoEEyyZGxT5kLITfqkOgn9K5Yi6uB4BWVSsfdeQgcNv2po-t8b5umyOs0BOD2M0pUfv1H0RRvI_KeZ3icjBIVvwrzWk7U_0QdriOPTDw8UtNebc9olqbl0vWKqGg0u37yGtGA5Gb7vy2EgH6Mys3HaeqSXocPinchKl5s4zKYgHxK_nchQ9XBHFmgQuUtdO-UnZ3Nmq-ou5cKbJ2c14SCGnIR8WJtJKI9XZAPGysNTrsd1RpoBNpaki-KGHp8CRNiOK1iDt4nFlLSwUXejfepae4z2VhG_54A/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Fpub%2Fdist%2Ffreesurfer%2F7.4.1%2Ffreesurfer-macOS-darwin_x86_64-7.4.1.pkg
After installing 7.4.1, you should run the fs_install_mcr_script provided in 
the freesurfer distribution to install and setup R2019b using the instructions 
below.
- R.

$ export FREESURFER_HOME=/Applications/freesurfer/7.4.1
$ cd $FREESURFER_HOME/bin
$ sudo FREESURFER_HOME=$FREESURFER_HOME  ./fs_install_mcr  R2019b
… answer y to any installer questions ...
The script should output how to set the environment variable LD_LIBRARY_PATH to 
pick up the The MathWorks libraries.  That might include a setting 
something like, $ export 
LD_LIBRARY_PATH=$FREESURFER_HOME/MCRv97/bin/glnxa64:$LD_LIBRARY_PATH
Please make sure you have otherwise removed any references to your previous 
matlab R2016 environment from PATH, LD_LIBRARY_PATH, etc. 

On Jan 29, 2024, at 21:02, Iglesias Gonzalez, Juan E. 
 wrote:Dear Joao,I’ll defer to our 
software specialists, but another option may be trying the Python 
version:https://secure-web.cisco.com/1gPJbJkeAwLxRG5ISVgM2USwM6OoyR8xf1PZE6EvMJf-SRaA9EGrMIWMtoTGH7aMT86QE3DlUA-XL1cyKUT3DHiXT0ma5mZHgd8ElXQmslT_wo-B2jePlem_KHUlWQToIJfu88U9chsrSFPXs215vnwwuXBvNTLJVE_lh4T6cIBV8QanuQVm3e3BjQ2EaXcYC6lhhkrsO-307Mn1YWFWI0xkVANXmWcY12KiGHnlfDB4oQwY-GjBYbyVDhcDlyZNNNweBWf11saa25eKp5Psjr8CU3zE-iQlD181J1MMo6K2lE_R2hvTnJn_7VjLF8-XpGoq_UscsjzCYr00bk4ySXg/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FSubregionSegmentationCheers,/E  --Juan
 Eugenio 
Iglesiashttp://http://secure-web.cisco.com/1xkFYctwFMfhxok7RYaJbrw5crH_Wnw2ywE2VZjqP-qYTzxO45GiX_q_jHOGkqPmOQY12cjT47WY_TNufoQOmeAFinHtebu_tDtkJJVMmB96rzEQOlCZI1k2mTTmKDvUzHaDMbEkw4eLcStBv9BFy5ovxP_UcPTbUqlRjlE6blbq8D5Fv7VSm30vX9EUttKo8iDtVUGfS2XjFHB6gAGXA1URsH0JKHt7Q7dflcHZH_NjOHpx0Yn-QKiwXl_S6b6qeUhvyqWOImXysYCX2OZ2FK_hd1KwrVcATlaLNfRrLWT-3UAWR26hK9Kd627pXbyVKblH7o-d5_SZJqNciPeKwBQ/http%3A%2F%2Fwww.jeiglesias.com%C2%A0From%3A%C2%A0freesurfer-bounces%40nmr.mgh.harvard.edu
  on behalf of João Ramos 
Date: Monday, January 29, 2024 at 4:26 
PMTo: Freesurfer@nmr.mgh.harvard.edu 
Subject: [Freesurfer] longitudinal 
hippocampal segmentation error in Mac OS Sonoma + Freesurfer 
7.2.0External Email - Use 
CautionDear all,I would 
appreciate your help in an issue I am having and one that I have not found a 
reference to regarding Freesurfer. Basically, I have run all of the 
longitudinal Freesurfer pipeline and I am now interested in running the 
longitudinal hippocampal / amygdala segmentation code (segmentHA_T1_long.sh), 
though I am faced with an error (log below). I have searched and this happens 
on various settings with no pattern that I could recognize (apart from iOS app 
development), and it was also pointed out on a mathworks forum post regarding 
matlab 2016 on a Mac OS Sonoma (which is my operating system, and this version 
of freesurfer uses matlab r2014b). Would this be possible to run within Mac OS 
Sonoma (v14.2.1, with current freesurfer version 7.2.0)  or should I 
run a linux instance with freesurfer install and everything?Thank 
you!USER joaoHOST Joaos-MBP.lanPROCESSID 
17239PROCESSOR x86_64OS DarwinDarwin Joaos-MBP.lan 23.2.0 Darwin Kernel Version 
23.2.0: Wed Nov 15 21:54:10 PST 2023; root:xnu-10002.61.3~2/RELEASE_X86_64 
x86_64--##@#
 Longitudinal Hippocampal Subfields processing (T1) left Mon Jan 29 20:55:28 
WET 2024--Setting up environment 
variables---DYLD_LIBRARY_PATH is 
.:/Applications/freesurfer/7.2.0//MCRv84//runtime/maci64:/Applications/freesurfer/7.2.0//MCRv84//bin/maci64:/Applications/freesurfer/7.2.0//MCRv84//sys/os/maci64:/Applications/freesurfer/7.2.0//lib/gcc/lib:***
 Terminating app due to uncaught exception 'NSInvalidArgumentException', 
reason: '-[__NSCFString stringByStandardizingPath]: unrecognized selector sent 
to instance 0x62e281b0'*** First throw call stack:(

Re: [Freesurfer] recon-all cannot execute: required file not found

2024-01-19 Thread fsbuild

External Email - Use Caution

I don’t see what FREESURFER _HOME is set to, but if you used the .deb package 
installer, it would be /usr/local/freesurfer/7.4.0, i.e.
$ wget 
 https://secure-web.cisco.com/1vzo5wK6ItFFFMnllsCMKRTIzcqYXDSETeXibiyz78VEk_TVHkbVLtjlltPd0g0Uvd8x0WK89GE8gU1KWFMzKnfwwgiI7LxjmgavQJ6CRuDKNdbu69lRngmJXHI_jT7Apzbthify1jBVr0Rl4tHRLO59uiYFLhP5xVv4FxnW-1brLM5t_f80dYxYqxS-tDJmUcSQBJ26bUuIwdNXHT49QU9R4-QLIUjxabN7pBG7dNNvYjk6etULRIlRTmLlKSxZ11x1M0Be8QDGN-sL353J66YtQqcu9Ew-9KlI2nYNXikCfbW-0PZolvzHu35pUzJw_8zpHpyEpfdmLOKtTKWv0Iw/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Fpub%2Fdist%2Ffreesurfer%2F7.4.0%2Ffreesurfer_ubuntu22-7.4.0_amd64.deb%24
 sudo apt-get install ./freesurfer_ubuntu22-7.4.0_amd64.deb… answer yes to all 
queries ….,.. output deleted ...
$ export FREESURFER_HOME=/usr/local/freesurfer/7.4.0$ source 
$FREESURFER_HOME/SetUpFreeSurfer.sh … output deleted …
$ which recon-all
/usr/local/freesurfer/7.4.0/bin/recon-all
$ recon-all -version 
freesurfer-linux-ubuntu22_x86_64-7.4.0-20230510-e558e6e
If you used the tar file instead, then some permissions might not be correct 
depending upon how/where it was unarchived (and some dependencies might be 
missing).
- R.

On Jan 19, 2024, at 15:20, Peled, Noam,PhD  
wrote:I'm just trying now to run the "recon-all -version", also without 
any arguments. Both produce the same 
error.Thanks!NoamFrom: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Huang, Yujing 
Sent: Friday, January 19, 2024 3:10 
PMTo: Freesurfer support list 
Subject: Re: [Freesurfer] recon-all 
cannot execute: required file not found I’m wondering how you ran 
recon-all.  Do you see the error even running it w/o any 
arguments? From: freesurfer-boun...@nmr..mgh.harvard.edu 
 On Behalf Of Peled, 
Noam,PhDSent: Friday, January 19, 2024 2:59 PMTo: Freesurfer support 
list Subject: Re: [Freesurfer] 
recon-all cannot execute: required file not found Thanks Yujing,Yes, 
I looked for the file permissions using ls -l. It does have execute 
permissions.I also tried running chmod which didn't 
help.. Thanks,NoamFrom: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Huang, Yujing Sent: Friday, 
January 19, 2024 2:54 PMTo: Freesurfer support list 
Subject: Re: [Freesurfer] recon-all 
cannot execute: required file not found After sourcing Freesurfer, 
$FREESURFER_HOME is added to the front of your $PATH. 1. ‘ls -l 
$FREESURFER_HOME/bin/recon-all’ to check if your recon-all has the execute 
permissions?2. use ‘chmod +x $FREESURFER_HOME/bin/recon-all’ to grant the 
permission  Best, Yujing From: freesurfer-boun...@nmr.mgh.harvard.edu  On
 Behalf Of Peled, Noam,PhDSent: Friday, January 19, 2024 2:42 
PMTo: freesur...@nmr.mgh.harvard.eduSubject: [Freesurfer] recon-all 
cannot execute: required file not found Dear group,I'm trying to run 
Freesurfer on digitalOcean server running Ubuntu 22.10 (GNU/Linux 
5.19.0-46-generic x86_64)I Downloaded freesurfer 7.4.0 
(freesurfer-linux-ubuntu22_x86_64-7.4.0-20230510-e558e6e)After sourcing 
Freesurfer, recon-all gives following error:.../freesurfer/bin/recon-all: 
cannot execute: required file not found Other functions, e.g. freeview, 
mri_info, all seem to work as expected Would love some 
help.Thanks,Noam  ___Freesurfer
 mailing 
listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail.

Re: [Freesurfer] recon-all errors (cannot execute binary file +

2024-01-16 Thread fsbuild

External Email - Use Caution

It looks like you did not use the .pkg file installer to install Freesurfer on 
the Mac, otherwise you would have a path like /Applications/freesurfer/7.4.1 to 
use as FREESURFER_HOME.  The installer should ensure the privileges should 
be correct to run commands.   There are several 7.X freesurfer releases, 
but the latest release is 7.4.1 and you can download it via the link, e.g.,
https://secure-web.cisco.com/1bTTDiznaFEJgJPDoi2yskrFqRdt_lNsr8LZ0PFjdBlc19JuHE6WaWHssFDdzwRLVMRUHA3qj7h4ea64BhZk97t2IniNpnSEBUfevruwnZRT-WXrHBzlmbnxwfB-eUVqRKZYuKEwgZupdFOKnrwiz0xxPKw5DTxfL31t8mtljoZBWCtHjo8uXtSylGlGyZRzw2b6Kjz5JBf1zzrJTR_GSBoP7UPjKW3-cqENylh36UvAaYHpdFnPoZ4CrWPzQwkw7vmD7cmQcG6jBsy_w7nUkvkrhCZTYVfLg5BUluX8L0H85LGn_CikykHFVbAsE-L8Zih6Q9g6D25IvisceU2Rl_g/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Fpub%2Fdist%2Ffreesurfer%2F7.4.1%2Ffreesurfer-macOS-darwin_x86_64-7.4.1.pkg
I would first remove what you have on your system from the terminal window with,
$ sudo rm -rf /Applications/freesurfer
Then in a Finder Window navigate to the Downloads folder (or to wherever you 
downloaded freesurfer-macOS-darwin_x86_64-7.4.1..pkg).  You should be able 
to RIGHT CLICK on that file, select open with the default pkg installer, and 
then enter your password etc. to install it.  Right clicking should bypass 
having to do some of the security exemptions in system preferences.
Once the install is complete, setup the Freesurfer environment in the terminal 
window,
$ export FREESURFER_HOME=/Applications/freesurfer/7.4.1$ source 
$FREESURFER_HOME/SetUpFreeSurfer.sh 
freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 
Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME   /Applications/freesurfer/7.4.1
FSFAST_HOME       /Applications/freesurfer/7.4.1/fsfast
FSF_OUTPUT_FORMAT nii.gz
SUBJECTS_DIR      /Applications/freesurfer/7.4.1/subjects
MNI_DIR         
  /Applications/freesurfer/7.4.1/mni
You also need a license file, license.txt.  Once you complete the license 
request form 
at https://secure-web.cisco.com/1Svw39fuKLV2rL8mAOfpPDMZrLLodE_ScR0sKC5od9QRlt9jwKuDUSQ6WtLlT9V17W1wUaBdznmlv7nMRbyPA6LYSYXyCAnP8F-Tuz_VE6STeVAxkh40QhJ8_Hz3w6xgC49SELup9uGscJnea_a5_YfPe4v_s5sGckdUErRUBLgOMN41ow4CikTKbC-IfUIre0ikhv0rLYF0iFjK9EZGFCuzHN7-z5cvA1mPBIjRTyGJsmV-behjR7Zpaho6a5uOuq1I4CB61WxtecgERQIEuY6PCEpMSMO1vfX-v7GEXY61w_SZ_5yg0kRQoolU2kwNaTPReDO7q7kH9B3AAFtRMPQ/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Fregistration.html%26nbsp;you
 will receive a file “licesne..txt” via the email address used in the form. 
  Download/copy the license.txt file to your machine from the email.
If your home directory is for example /Users/hyejung then you will see the 
following in the terminal window,
$ cd$ pwd/Users/hyejung$ echo $HOME/Users/hyejung
… if you downloaded license.txt into your Download folder ...
$ cd Downloads$ ls license.txtlicense.txt$ cp -p -f  license.txt 
 $HOME/.$ cd $HOME$ ls license.txtlicense.txt
You could also use the Finder to navigate and drag/drop the license.txt into 
your home directory.   Once it it there, set the environment variable 
FS_LICENSE so freesurfer commands will find the license when they run,
$ export FS_LICENSE=$HOME/license.txt
Then it should work to run freesurfer commands from the terminal window 
including freeview.
- R.

On Jan 16, 2024, at 20:47, 윤혜정  
wrote:External Email - Use 
CautionGood day.When I run 
recon-all for my nii files I get either one of the following error 
messages:1. ERROR: could not configure recon-all parameters 
Killed 2. ERROR: could not configure recon-all 
parameters /Applications/freesurfer/bin/fspython: line 20: 
/Applications/freesurfer/python/bin/python3: cannot execute binary 
file /Applications/freesurfer/bin/fspython: line 20: 
/Applications/freesurfer/python/bin/python3: Undefined error: 0Or 3. a Pop 
Up message "_struct.cpython-38-darwin.so" cannot be opened because the 
developer cannot be verified. mac OS cannot verify that this app is free 
from malware. I googled the third error message and tried "Allow 
anyways" from the privacy setting. Then the next message pops up, 
then the next and the next. Could you please help me to understand the 
cause of the above 3 error messages? I tried to redownload freesurfer as 
well as python but none worked. Thank you in 
advance. Best,Alice___Freesurfer
 mailing 
listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means yo

Re: [Freesurfer] Freeview crashes when trying to load volumes

2024-01-15 Thread fsbuild

External Email - Use Caution

It would help for us to know what your machine is running, e.g., linux or
MacOS (Intel or Silicon Mac) - and what the version is for the operating
system, e.g. Linux Ubuntu 22, MacOS 12, etc. If you are running Linux on
Windows thru either WSL or a VM then please mention that and if the Windows
host is running Win 10 or 11.
- R.
On Jan 12, 2024, at 11:52, Ford, Jamie K
wrote:External Email - Use
CautionHello,Please could I get
some advice on my installation? I've downloaded version 7.4.0 using the same
steps described in the installation video MailScanner has detected a
possible fraud attempt from "secure-web.cisco.com" claiming to
behttps://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall?action=AttachFile&do=get&target=installFS_demo.mp4 Everything
seems fine until I try to load any sort of volume, e.g., a Bert MRI file (like
on the video). Freeview then crashes. This is the same for any
volume. Could someone please advice? Any guidance would be greatly
appreciated.Many
Thanks,Jamie___Freesurfer mailing
listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Please note that this e-mail is not secure (encrypted). If you do not wish to
continue communication over unencrypted e-mail, please notify the sender of
this message immediately. Continuing to send or respond to e-mail after
receiving this message means you understand and accept this risk and wish to
continue to communicate over unencrypted e-mail.

Re: [Freesurfer] Trouble with ssh tunneling & Freeview

2024-01-11 Thread fsbuild

External Email - Use Caution

A remote connection working to display images from the glxgears or xeyes 
commands run on the linux host forwarded to your local machine does not mean 
Freeview graphics will do the same.  If Freeview still displays an empty 
or black screen, then there could be issues with OpenGL graphics running on or 
being sent from the linux host.   The system requirements for Freesurfer 
include the following for running Freeview,
Graphics card: 3D graphics card with its own graphics memory 
& accelerated OpenGL drivers
Updating the OpenGL drivers on the linux host will sometimes enable Freeview to 
display images remotely.  My understanding is Linux servers need Mesa 
packages installed to support newer versions of OpenGL.  If the Freesurfer 
Debian or RPM package installer was used to install the Freesurfer distribution 
on the Linux host, then at least some of those packages should now be 
installed, i.e., we do not recommend using the tar archive to “install” 
Freesurfer.  We don’t know how EXPANSE installs/maintains Freesurfer or 
what their servers support for graphics hardware.
GLX is the X-windows extension for OpenGL graphics that can be tunneled thru a 
remote SSH connection.  But GLX may not work with the newer versions of 
OpenGL over ssh.  A workaround for this is to install and use VirtualGL on 
the Linux host.  If VirtualGL is supported/installed on EXPANSE, try 
prefacing the freeview command with “vglrun” - 
see https://secure-web.cisco.com/10kzDiIcCSK5wSi3KZ4WHry8djBXAuam589oKZqs5TvrpZwtx_bg2pMLPYhP8Jy_MCc-EzDmY-dqikD_6634fXGIuWxPmIpVKc_7FvQJ1WLhxdWKQNREcPKVjjXtooJBwDbQMYGNkRFTt8kV6opy3zDRKCw2VFxn2ADZvwE-CJh_5FiVuijgz3-BKzUFkbC6C6v0BjwjdzAd3rvsTA-OMSKycamq6dtAADv6xzHGy1pd8-jWOBWz55-o6eUCbotpP3Xjkaj44Yj6JNn9W87mEonAk4nFRD7f8ZUJdi0BwhynYiOrU-XXN9NEleN4SBmflmdoT6sWwWvQHcooLyMlnww/https%3A%2F%2Fwww.starnet.com%2Fhelp%2Fvirtualgl
  We use VirtualGL and graphics acceleration on a few Linux workstations 
to accommodate Freeview running on Linux and viewing its 3D graphics thru a 
remote VPN connection.
XQuartz on the Mac is the equivalent of X-Windows on Linux.   The Mac 
should be using Xquartz 2.8.2 or newer for use with the Freesurtfer 7.4.X 
releases.  I think X-Quartz will open automatically to view X-Windows 
based graphics on the Mac.
If the EXPANSE linux machines are setup to support remote connections to view 
3D X-windows graphics then the IT support staff will know about the options 
above.  File/open a ticket with them, ask them what they support, and how 
to setup your environment.  If they do not support it, an alternative is 
to install Freesurfer on your Mac and download/copy over the data to view with 
Freeview.
- R.
On Jan 11, 2024, at 14:18, Dong, Yilei  
wrote:External Email - Use 
CautionHi Freesurfer 
team, I have Freesurfer installed on UCSD's Expanse HPC, which uses the 
Rocky Linux 8 operating system. Whenever we try to do ssh tunneling and more 
specifically, logging into our HPC via ssh -X to open up Freeview's GUI, it 
always aborts. Prior to logging into my HPC from my Mac laptop's terminal, I 
always open up XQuartz. Another colleague of mine has also encountered similar 
issues, where they have managed to get X11 and Xeyes to run, but also 
Freeview's window keeps aborting. We have also tried to follow 
instructions from the following links when it comes to getting ssh tunneling to 
work correctly in hopes of making Freeview's GUI pop up: MailScanner has 
detected a possible fraud attempt from "secure-web.cisco.com" claiming to 
behttps://http://secure-web.cisco.com/12UaY28IjOvcCuzqwhVkemgeWWYzbyjV_gOl5bvSd-xgSy77ILuGBhPY6qPumJh0zLPo9B1IddZ-5F3ldYWW9jnrPdNM07lirk88wNgJrzWex0cuUCHsmM03NfVHfywusHDbKGei7iUd2RNw0Wj4tZBh8IZM0hK3N-EeXuQktbpl22fBLF8A6ZK6nbgwtaTd-UgPuGxht7pJQ5dZnPQa9ZgYj5vFk-oQNlJQJVrUQDdAu1IsSKk7-3J0xIpZGIQ3p--LPjQXvLyuurp_vQb8U7xdYkC62sEVtr7LY4ux8fTPog7UyA5usa_m75oyYIGwT54qTXS-AXEh5GS-632IA9w/http%3A%2F%2Fwww.nmr.mgh.harvard.edu%2Fmartinos%2FuserInfo%2Fcomputer%2FremoteAccess.php%23graphicsMailScanner
 has detected a possible fraud attempt from "secure-web.cisco.com" claiming to 
be https://secure-web.cisco.com/13jhlKniK4ot1jAvrTEdLmUxfeVBEFlM0Xf3YMvRlE0gq6-vGRZz3p6eV2ZQx5RS0jNCj_reYJBdnIcOVavR5zgBEVioq5stB9hydwZvyzokRjSpJYL0wreyNtjPUlutWSbgoC8i5cbU7qN-8grDPZs-myayIL4VnGNebEO41TgXHT6EYseYu18uBPPkpaZlk4J85BkLvHnhjyuL5B2D2K9uuUkzNMNwKO-hl3br0t2sF_PstW8EW_V08RHiHyv1qmjj7Ju5Pr1ZAXQwmHG04EKPzZJZ2Fnr41B5GEGTg0ukJqIK41n_9n45WEU_JwntnaTEprGkgVxI90r9lG8fVsA/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FRemoteAccess.%26nbsp;If
 we operate from a Mac computer, is it better to use a VNC or XQuartz for ssh 
tunneling? In addition, can we find an error log in Freesurfer's directory to 
find out exactly why Freeview keeps aborting in our circumstance?Thank 
you. Sincerely,Yilei ___Freesurfer mailing 
li

Re: [Freesurfer] Scratch Directory Permissions Denied

2024-01-09 Thread fsbuild

External Email - Use Caution

 Is SUBJECTS_DIR for Freesurfer being set to live under a temporary 
scratch directory initially created by and then subsequently used by Matlab?
If so, maybe Freesurfer is deleting files and/or changing file permissions 
there - causing Matlab to subsequently complain.   I would not expect 
multiple programs writing to the same directory tree to work together if they 
use different file permissions, privileges, and/or perform independent 
clean/delete functions in shared directories.
- R.

On Jan 9, 2024, at 14:47, Michael Ruvalcaba 
 
wrote:External Email - Use 
CautionHello,I am trying to run 
the recon -all function in my MATLAB pipeline using Freesurfer 6.0.0 and I 
have no issues with it. However, when I run the recon -all step using 
Freesurfer 7.2.0 and run the following command (the recon -all step finishes 
without error by the way):ft_read_mri([subdir 
'3D_Images/freesurfer_pre-op/freesurfer/mri/T1.mgz']);I get the following 
error: /bin/bash: 
/scratch/tp746feb5d_1e83_4141_b25d_1824a1cb209e.load_mgh.m.mgh: Permission 
deniedThe issue is there is no scratch file and it looks like between version 
6.0.0 and 7.2.0 there is some extra lines of code that uses a scratch directory 
(which 6.0.0 doesn't)Does anyone have any input on this? I hope this made 
sense!Best,Michael 
Ruvalcaba___Freesurfer mailing 
listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail.

Re: [Freesurfer] Freeview keeps aborting.

2024-01-09 Thread fsbuild

External Email - Use Caution

I would check with your IT support staff about the error including asking
if the machines in your cluster are setup to display X Windows sessions with
image viewing applications like Freeview. If the machines support
remote graphics, they should be able to tell you what you need to set in your
terminal session for it to work. But it could be they expect
programs like freeview to run on your local client machine and read the image
files/data over the network via NFS, etc.
- R.

On Jan 9, 2024, at 18:52, Dong, Yilei
wrote:External Email - Use
CautionDear freesurfer
help, I have freesurfer installed on UCSD's Expanse HPC, which is on the
Rocky Linux 8 operating system. Every time I try to open freeview, it always
keeps aborting. How should I fix this so that freeview's GUI can be shown? I
have included the screenshot for reference on the error. Thank
you. Sincerely,Yilei ___Freesurfer mailing
listfreesur...@nmr.mgh..harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] Infant fs

2024-01-08 Thread fsbuild

External Email - Use Caution

Sorry I cannot address those questions for you, but I have sent your
email along to one of the developers.
- R.

On Jan 8, 2024, at 19:17, Amrita Pal <palamritaor...@gmail.com>
wrote:External Email - Use
CautionThanks. I had filled out
the form. How long do they take to respond? Also can I do subcortical thalamic
segmentation with it? How is the LUT calculated both for infants and adults?
Would you recommend an eleven year old's data analyzed by regular FS or infant
FS?On Mon, Jan 8, 2024, 6:19 PM fsbuild <fsbu...@contbay.com>
wrote: Looks like you need to fill out the request form,MailScanner has
detected a possible fraud attempt from "secure-web.cisco.com" claiming to
behttps://surfer.nmr.mgh.harvard.edu/fswiki/infantFS- R.On Jan 8, 2024, at
18:12, Amrita Pal <palamritaor...@gmail.com>
wrote:External Email - Use
CautionHelloI am trying to use
the infant fs for processing my pediatric data. Where can I download the
package?Thanks and
Regards Amrita___Freesurfer
mailing listfreesur...@nmr.mgh.harvard.eduMailScanner has detected a possible
fraud attempt from "secure-web.cisco.com" claiming to
behttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer___Freesurfer
mailing
listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard..edu/mailman/listinfo/freesurfer

Re: [Freesurfer] Infant fs

2024-01-08 Thread fsbuild

External Email - Use Caution

 Looks like you need to fill out the request form,
https://secure-web.cisco.com/1Zztv_hv2CHwkWkqDcQ75P0iZ5m3guJnkq6OOGA_AuaX-IiyZb0WPr8KCpekneZq3xdVmuMPM23fTG3Ht7xu0ZxxuE7lX3v7MtXKhOYdch26VavRXmE4TYyFgzUtcfZ8Mh10uPUrEamBqumy-FNcsmw7X_b2F1UYP4c2d7gcvt63cz8GX-LgMtaXaMwavAIFqEGWOWCd96T8ZnjtbulPm0DPyZmtcSrfnpR6765ew-pjl__K7VbzCX08ymTl8j_cLhGOLEch-DlM3gKLQeqKQZIr8dYWNag83n8Gk-CILxUMV-m5nRv5XliC_fxFPkjVewauJwD8Y04ZXBm_jIlWxOw/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FinfantFS
- R.

On Jan 8, 2024, at 18:12, Amrita Pal  
wrote:External Email - Use 
CautionHelloI am trying to use 
the infant fs for processing my pediatric data. Where can I download the 
package?Thanks and 
Regards Amrita___Freesurfer 
mailing 
listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail.

Re: [Freesurfer] Subject does not have a bstampfile

2024-01-08 Thread fsbuild

External Email - Use Caution

  Let me add that it will not work to use shared mount point from the 
Windows filesystem as you list below,
/mnt/c/Users/GCM/Desktop/subjects/NowakG/mri
-
 for your SUBJECTS_DIR when running a recon-all command.  The command 
will fail because the Windows file system does not support soft-links.  
 Any SUBJECTS_DIR used for recon-all needs to be inside the Linux OS 
image running freesurfer.  You could however copy the files from that 
mount point to create another SUBJECTS_DIR somewhere inside your Linux 
image, e.g., under your home directory in linux.
 in your linux terminal window ...
$ cd$ mkdir subjects$ export SUBJECTS_DIR=$HOME/subjects$ cd $SUBJECTS_DIR$ cp 
-p -f -R /mnt/c/Users/GCM/Desktop/subjects/NowakG .
- R.

On Jan 8, 2024, at 16:10, Huang, Yujing  
wrote:You need to specify the input files to process. Here is the wiki page for 
recon-all - 
 https://secure-web.cisco.com/1hqVY7QioPnD85rxOcGMUcCuynnW47DWZwkPX0Z-CZpPZhsuOE3Dqq56yZOR48pnqlARbSGSU1uJNTssTzOLeJZDej-4B4APtXHQmIDTAeNiz6injsGyGghBE4szgzC-CIvlktYVKAeIFD9vBNBZGTgRtRAfcxOZTJJXzk0kPtE9fSY8vo9o05Q8Lf5La4t7Av6IvB6hkO3ZqlfaDGIxlZfRhNJC0f5oWDNXpfp8nYykG-egLh8zOuhOsHSbWCac7UKV67GamZPc5FS5KwH3vo_4_Omj5v0dIRxZ5O4d9WtJGN0f3IkrLaqnXHmnqhmI4YmYtNQmp-0UBF38a-xfw4w/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2Frecon-allBest,Yujing-Original
 Message-From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Joanna KidonSent: 
Monday, January 8, 2024 3:33 PMTo: freesur...@nmr.mgh.harvard.eduSubject: 
[Freesurfer] Subject does not have a 
bstampfile   External Email - Use 
Caution    Hello FreeSurfer 
Developers,I'm attempting to compute Segmentation of hippocampal subfields and 
nuclei of the amygdala (cross-sectional and longitudinal), as described on the 
https://secure-web.cisco.com/1JRIAQtmLphlXIykU3RsSWy2GeEv_y0Em3hHjyX02njKQRMzktRXyIr6AsUKD8-6mfnHs3e3VqgraV5HY65g0kcdnn-c5SO11uj3GmVopw6uBvHuq9nL41NZthselkwcmF1_pfF7tqA1mMsAKXVbGF7kWv-nHwevhhA8F6Ut_G89GsS36wOdw4Qdt0y3NAVk7FFD73D5O1AlLLXsiM0_emjpApIZBLEppGP5jjmBYXvnW-lkYFHOz1Mpazf7b7a-Tkol4Hrp9s-ygaeijb4CyTVrQYXiaqfwLwo5L2QmewMDyINYXoiDYTFnRY1ZnSd75iVr_Rv6sEbBi2merzCpAuQ/https%3A%2F%2Fsecure-web..cisco.com%2F1thysYb_zO3z1vpgSTaPhhhrJHE6mFgjDwcJg3vFCVfZAwtvXgTVrtcAutSPTrtciZPyxNbynvc15Hs2QuWbY_5s83lqlEQoYQJki7l_TF3oztafbzs30sHpSw0h-eZSPjzJ5uVCT29lxgi-ynPEhcVbMEKprxj8oqXGxzhvsFrvGlrQlowS673v0V1k05awg3ja96pJZpAes0ADbo-3Cdp-F5Ia5oD5q7fabDh5N202LPH9PNC1ruPvKvy_5987OSpV7RTftXJev5hauvVESrxnACVsA0f5bGY-t55yLWz2a-Tkq1eIulXgNxAa228gMMBHaDYc4X4fiJjG0re3rdg%2Fhttps%253A%252F%252Fsurfer..nmr.mgh.harvard.edu%252Ffswiki%252FHippocampalSubfieldsAndNucleiOfAmygdala,but
 I get the following error when I run the recon-all -all -s command:Subject 
does not have a bstampfile, copying 
/usr/local/freesurfer/7.3.2/build-stamp.txtSubject FS 
Version: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275No 
constraints on version because REQ=UnSet and FsVerFile=NotThere #@#% 
fs-check-version match = 1 fs-check-version DoneINFO: SUBJECTS_DIR is 
/mnt/c/Users/GCM/Desktop/subjects Actual FREESURFER_HOME 
/usr/local/freesurfer/7.3.2 Linux LAP-LKP 5.15.133.1-microsoft-standard-WSL2 #1 
SMP Thu Oct 521:02:42 UTC 2023 x86_64 x86_64 x86_64 
GNU/Linux##@# MotionCor Sun Jan 
 7 20:48:46 CET 2024ERROR: no run data found 
in/mnt/c/Users/GCM/Desktop/subjects/NowakG/mri. Make sure to have a volume 
called 001.mgz in /mnt/c/Users/GCM/Desktop/subjects/NowakG/mri/orig.If you have 
a second run of data call it 002.mgz, etc.See also: 
http://secure-web.cisco.com/1YoN1A69KdRcMav_4NI9T7PYgKG5FAtbmkvQ7vxtAUykGwuliarvPShgKfL_ItgaKWWnaYhDjK5FMWmDuPGEEEjW91LA3z7KDEeMiaIfV2jyXtfoUeeAjtPetkV6AuryGQBEKfk8d73IpHcgRIPrySwzLQaUtJT-A3dciz-Ma0n5qP4wsp5g9Tjvw5bGZUJlDFhJwWQrn04-RanD9XSLv0hlRr6ygjNO1BDIi4FgyjW3UWknkdWZwG9r4rG9cdS5Q0g6fBJ_QfVYe1DlgOs71lVji4Q7vMKZoWhEAgKq_5yhthldQEcJLHUmFLDrBcBX1TXcVwnrmkcLYG8z3GWHohA/http%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsTutorial%2FConversionLinux
 LAP-LKP 5.15.133.1-microsoft-standard-WSL2 #1 SMP Thu Oct 521:02:42 UTC 2023 
x86_64 x86_64 x86_64 GNU/Linuxrecon-all -s NowakG exited with ERRORS at Sun Jan 
 7 20:48:46 CET 2024I've searched the list and no similar errors have been 
reported. Does anyone have any thoughts on how to trouble-shoot this one? Also, 
Ive attached the scripts/recon-all.log in case it's of any use.Best 
regards,Joannadr
 n.med., specjalista fizyki medycznej, neurobiolog Przewodnicząca Sekcji 
Diagnostyki Obrazowej Polskiego Towarzystwa Fizyki Medycznej Zakład Kardiologii 
Inwazyjnej i Elektrokardiologii, III Katedra Kardiologii Śląski Uniwersytet 
Medyczny w Katowicach Kierownik Działu Fizyki Medycznej, Koordynator ds. 
Ochrony Radiologicznej Z-ca Kierownika Zakładu Diagnostyki Obrazowej 
Górnośląskie Centrum Medycznego i

Re: [Freesurfer] Tksurfer and freeview

2024-01-06 Thread fsbuild

External Email - Use Caution

 tksurfer has been deprecated and essentially replaced with 
tksurferfv bash shell script which runs freeview.   But whether 
or not you run the front-end tksurferfv bash script or the freeview 
command directly, I’m not aware of an option whereby you can tell 
freeview to run tcl/tk scripts.  My understanding is running 
tck/tk scripts as the -tcl switch allowed in tksurfer - is not supported in 
freeview.
- R.
- - - - - 

$ tksurferfv --help

This is a script that runs freeview with arguments like tksurfer.
Not all tksurfer functionality is replicated.

tksurferfv subject hemi surface 

-tksurfer : use tksurfer instead of freeview
Can have multiple annotations

-all : load white, pial, inflated
-vgl : runs freeview with /usr/pubsw/bin/vglrun
-no-vgl : does not run freeview with /usr/pubsw/bin/vglrun
-no-outline : do not show annots as outline
-neuro : use neurological orientation instead of radiological
-rotate-around-cursor (-rca) : in 3d view, rotate around cursor (use -no- to 
turn off)
-linear, -linearopaque, -piecewise, -min_to_max (default) : overlay heat scale

tksurferfv dev


On Jan 6, 2024, at 20:59, JAEHYUN KIM  
wrote:External Email - Use 
CautionHello,I attempted to 
switch tksurfer to freeview in the script, but it seems like I need to change 
arguments "tcl" to something that can be applied to freeview.Option 'tcl' not 
recognized.What argument could possibly be used to replace tcl in the 
script such as tmp.tcl and lh pial 
-tcl??Best,Ed___Freesurfer mailing 
listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail.

Re: [Freesurfer] recon-all -s SiroSTC006_pre exited with ERRORS

2024-01-06 Thread fsbuild

External Email - Use Caution

  

Your Linux image could be missing system files and/or graphics card driver 
updates needed for the version of Qt included with Freeview to display graphics
 via X-Windows.  So I would first remove whatever currently exists under
 /usr/local/freesurfer and then follow the instructions on the Wiki page
 to do an install from scratch using the actual installer (instead of 
the tar file).  The instructions are here,



https://secure-web.cisco.com/1aVasdKo9Pwif5UQ2Uch0IDTvauLowJGIckrOUQbXQ2UgjMTijxM2AHRnYW5Sikm1PLFsVxTugqk7jS8q66aPC2Wt61zvugIk0ou082bvW2Vi2HpkhPUVK5RuQZz2bLaagNV35aRFc1BnYpdMMEOV_I7Kv2taVGg0rdW4UYbH_GJbhgkvI-Qa_RFQ4NdxHnAc16p7Z3HD0wL3Y4ADaC0Bqe1RvUwRo4c9f42ae38IHeHekPpYi9ZUSGHQmOdCa1fI-XUD5NHGSIodtj96CXK30LHfH3-4qIZuhpUMifnii45pKrnP74W9KNsZeK4DZQ5G5nnKr6Vfy1E4qFgc-u2-qw/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFS7_wsl_ubuntu


After you install Freesurfer and setup the X-server on the Windows host -
 stop and verify basic graphics are working by running glxgears.  If 
communication from Linux running under WSL is working with the X-server 
on the Windows host, then you will see an X-Window open and display the 
spinning gears via the following Linux commands, 



$ sudo apt-get install mesa-utils

 answer Y to all prompts ... output deleted ...

$ which glxgears

/bin/glxgears

$ glxgears



The instructions on the wiki page end with running the "freeview" 
command with no arguments in order to test freeview can at least open 
and display an empty window.



If that works try displaying one of the volume files included in freesurfer,



$ freeview  $FREESURFER_HOME/subjects/bert/mri/brain.mgz



If that works, then try displaying one of your surfaces/volumes with your own 
freeview command.



If however glxgears worked, but the freeview command failed to open a 
window and/or display the volume as listed above, then the next step is to
 check for an upgrade to the OpenGL drivers on your Windows host.  
Freeview needs newer revisions of OpenGL in order to display graphics.  
Once you update the drivers, try running the freeview commands listed 
above again.



BTW - please remember to change SUBJECTS_DIR from 
$FREESURFER_HOME/subjects in your shell environment to a path your 
normal userid can write to w/o sudo/admin privs.  That could be in your 
home directory e.g.,



$ cd

$ mkdir subjects

$ export SUBJECTS_DIR=$HOME/subjects



You could put that export command in your shell init, e.g., $HOME/.bashrc file



- R.





On 1/6/24 13:25, Flemister, Abeoseh B. (flemist...@missouri.edu) wrote:






  
I’m using Ubuntu. 




Abeoseh Flemister

  

  
  From: Flemister, Abeoseh B. <flemist...@missouri.edu>

Sent: Saturday, January 6, 2024 12:24:40 PM

To: fsbuild <fsbu...@contbay.com>; freesurfer@nmr.mgh.harvard.edu 
<freesurfer@nmr.mgh.harvard.edu>

Subject: Re: [Freesurfer] recon-all -s SiroSTC006_pre exited with ERRORS
 
  

  


No, I installed using tar.gz





freesurfer-linux-ubuntu22_amd64-7.4.1.tar.gz










Abeoseh Flemister







From: fsbuild <fsbu...@contbay.com>

Sent: Friday, January 5, 2024 9:35 PM

To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>

Cc: Flemister, Abeoseh B. <flemist...@missouri.edu>

Subject: Re: [Freesurfer] recon-all -s SiroSTC006_pre exited with ERRORS
 

 
Did you install Freesurfer 7.4.1 using the Debian installer package ?

https://secure-web.cisco.com/1IOiqTlEkTSd5OYr_A3naRtVr5L_K5zRpteC0_uUt7M0gRolNr7VK3lsQcU_qofF0IDf9if55xJELV6MPMHK0trMuv6brwoSd7MfQJKQ0u8rG6GpC55LrWIvHRVZ5RLVajCat58QdOxjxETxHox8d-pjPklYqzufhatlnoff9JNXFQBE2YZu1fSh7A_UI7FYF5ow5QHCaq4mgE4HIWjw_RKbxKvWi44qi3wAXyIcVfJoZw9W_iaRleXKYVjeCJHON3xsxb9jOhTdZWl0OJXUj8PIarGpr4vFjOdYhQu0_VBCO9368S1QeeP4BRzeKe2J-ZEzfrbiiNKrP3ru0vjOGZA/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Fpub%2Fdist%2Ffreesurfer%2F7.4.1%2Ffreesurfer_ubuntu22-7.4.1_amd64.deb
- R.



On Jan 5, 2024, at 22:18, Flemister, Abeoseh B. <flemist...@missouri.edu> 
wrote:



External Email - Use 
Caution



Thanks, but the issue isn't that graphics aren't displaying, it's that freeview 
won't load because qt can't be initialized. 



Abeoseh Flemister



From: fsbuild <fsbu...@contbay.com>
Sent: Friday, January 5, 2024 8:27 PM
To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
Cc: Flemister, Abeoseh B. <flemist...@missouri.edu>
Subject: Re: [Freesurfer] recon-all -s SiroSTC006_pre exited with ERRORS
 

 
For issues with Freeview displaying graphics when running
 via Linux on a Windows host thru WSL, you could look at the recent 
thread with the subject "Re: [Freesurfer] Freeview not showing output", 



https://secure-web.cisco.com/1KBH0OQxJdEKdxK38EEhCdBUjp55VUN1FBiZ5YthIc5pA61hlHgbL-cEwJvdn2C

Re: [Freesurfer] mri_error_no_clear_message

2024-01-06 Thread fsbuild

External Email - Use Caution

If you do a case insensitive search for the string “error" in the log, you 
should see there are multiple listings of, 
IFLAG= -1  LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR 
RETURN OF LINE SEARCH: INFO= 4 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE 
INCORRECT OR INCORRECT TOLERANCES out of QuasiNewtonEMA: 008: -log(p) =   
-0..0  tol 0.10
This thread indicates it could be the skull stripping is not right, and should 
be 
checked,https://secure-web.cisco.com/1diiACwYbRU5h086AYSNGiqllYdOKITn3ySdC0K_QfnQR43A65qvLhyBqoue0bb2EIdQri_zKECQVz7Dg4n1y-KrqVKkY42kR7NxqLvFqeNGpT_LHmzYmFbyZcQarr8vTSInFpkA8dw2kifIJW092CogIViPRD29ux9nSFCHAFM-MjYDP7OR8RXAbFeqv5t3P9Y-GN-S8ou2NsWtfrhciLxc_rGRla71oL66AX4Rz8RTgJfYAKgsKItsVgU7_Ze_slOiVIeiN7awFuPLq1-2OpvYI9KsK-zyirB09oD4IW93nqNnKkerwb2Pkf2KVDYAm7eHdn_m0AZbg71elbxK9Cf3csOj7VWnmzRjt2G8KtiE/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg16992.html-
 R.

On Jan 6, 2024, at 01:10, yunus soleymani  
wrote:External Email - Use 
CautionHi Fargol,I recently 
heard about some problems from my coworkers who were using Ubuntu 18 and 
version 7.2.0 of the software. However, I am currently using version 7.2.0 on 
Ubuntu 22.04.2 LTS, and it works well for me. You could try it out and see if 
it works for you as 
well.bests,YunusYunus
 SoleymaniPh.D. Candidate of Neuroimaging Tehran University of Medical 
SciencesMailScanner has detected a possible fraud attempt from 
"secure-web.cisco.com" claiming to be MailScanner has detected a possible fraud 
attempt from "secure-web.cisco.com" claiming to be soleymani.yu...@yahoo.com+98 
914 526 
9298On
 Friday, January 5, 2024 at 10:05:54 PM GMT+3:30, Fargol Rezayaraghi 
 
wrote:External Email - Use 
CautionHi FreeSurfer Team,I 
hope this email finds you well. I'm trying to use a T1 image to get the 
aparc+aseg and wmparc nifti files. I was using this command:  
recon-all -s Subject1 -i T1.nii - all -notal -check ( I used recon-all -s 
Subject1 -i T1.nii - all first, and after getting Talairach error, I added 
-nota -check at the end).I'm getting the following messages without a clear 
error number: recon-all -s Subject1 exited with ERRORS at Thu Dec 14 
21:18:02 EST 2023For more details, see the log file 
/home/developer/Desktop/freesurfer/7.2.0/subjects/Subject1/scripts/recon-all.logTo
 report a problem, see MailScanner has detected a possible fraud attempt 
from "secure-web.cisco.com" claiming to 
be http://secure-web.cisco.com/1n6sdsWRV3TG8Jv2QrC7lr2OJkNo-vKWiVDfRMiE5lmXlfr-lokdvEt9eU6rLlP-aYqMbpq7K8EuAFgyM-6sO89wlS6SQyFVjfDrM7snkFk50KWtPcMrrMAb3-iDx3BvJzlzmHyj0ZOND6no-rksYRz4xSsFBN_9UnfKugJxeNypP2Hj8p3ohnddEIIXWWJiwXHUvl-q6ed-l--DVxtJuq-0q9GLNGkXfHafyVqJT-wYiKqyqa3_LTDndGHBRYVVjR3aNR8Yk5kzhAcfQ0V0xCnJghGvzLYBDnRmqqZBH_M2E4IbsaoFhxLjF6uz4KQphy-hq0G_fy4qWkLWvQOq0djR1FPNjJvPOTe0nl7LLpnQ/http%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FBugReportingThe
 version of the 
freesurfer: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76bMy 
platform is ubuntu 18_04_06 on Oracle VM VirtualBoxI've attached the log 
file. -- Kind Regards,Fargol R. Araghi (Rezayaraghi)Ph.D. Candidate, 
University of WashingtonDepartment of Mechanical EngineeringMailScanner has 
detected a possible fraud attempt from "secure-web.cisco.com" claiming to 
be http://secure-web.cisco.com/1MEbXNSnnv7NT1-4EzMYIfzctR98Iydj5J9JFwfH6Kv4xQ8RFYfNZ1-FLbFY0LR3b3gAbNVf39J834yCGuuDieCRxVv1PmsclTDaUtIvP9xcuHXFNd3SI-5JWP3t7QoQkPVjBDfSl5aO2ssQJ5uTSQybV2BUdc8ImY7AORL9Uz2P62vMPbegb42qe9ykB-sRrI0L5Hvjhaz6KWK9d3ewR-i9h-qytWo2MEFrrNCV3gMkYtzs5vPDIbtVNkBf9JFTVQSqFvD9o_KKDometmdLv2vgp7eHtjAswPZt6Q3W2L65Ckz2jrmXX5dknJ2nl0Dj59QdWnEGE7b-W4jR72W2lAXrMCnGVGRbuGml8G5qazXk/http%3A%2F%2Fwww.Kurtlab.com___Freesurfer
 mailing listfreesur...@nmr.mgh.harvard.eduMailScanner has detected a possible 
fraud attempt from "secure-web.cisco.com" claiming to 
be https://secure-web.cisco.com/1WLCgxPTXYmh2RXigsOXigGsIv-l-w5--kmcWP7kJObpHK9FXDq21o77qYl9AdDoGYEMxmuChf5AsdOpFr7I_LXXSl76fU-0LyWdSqeH_-GvoheZqN03QMF1E0hft-_ekH5QoEVLy42dlXU6lVHaw8GY-c3DU9kORjDVikyNoC-Sb55ubuw-wU9vEwnCAYIQyFKVvH7ktgJVubEBKURHckywY9-spiCuXt_Q58gxdP0Dc1mGkENS8luwjGCmVP9DBMCNJbI_el1sVc2OBXaZgGnUKDB6G2sCJ0Dz4S6TQpzTNBnpiFU0OWHE9qIB5xe--wbXX8jTEm0nRIzTLgNM5zQbgCYfkM-5CwOvEQR-rwKs/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer___Freesurfer
 mailing 
listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Please note t

Re: [Freesurfer] recon-all -s SiroSTC006_pre exited with ERRORS

2024-01-05 Thread fsbuild

External Email - Use Caution

 Did you install Freesurfer 7.4.1 using the Debian installer package 
?https://secure-web.cisco.com/1Q45DaXEMcahL0g3wyejOntK1tGwx5UNQU25fdIi6ImofQsUOBUFGOhQ21vBk8sDRQfWWELU7ghl6F8QsJA6G2LpBun8SBG8VuebFtJaMobqrOERog6kz0hiKLV9ajDE2AKC1cpczWaDYkcSc4gMj3M6RFSGVTMvswdtfRVwJb-Ck23miRyGdEEMqm_Vf-b-J9o0O3vxunBYSB4cBN28DNJm4do5FWUZ4zSzRajltNg7RZ46COiMaso4uOBO2RYGe0GsZu0-WtJ9Aceq0QL43ZSK1SlxBsNnkMA4gJsKlawl_Tl3esT3lDUmN4303CUV1bHuzWMUv-G-vhN66uSWjhA/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Fpub%2Fdist%2Ffreesurfer%2F7.4.1%2Ffreesurfer_ubuntu22-7.4.1_amd64.deb-
 R.
On Jan 5, 2024, at 22:18, Flemister, Abeoseh B. <flemist...@missouri.edu> 
wrote:External Email - Use 
CautionThanks, but the issue 
isn't that graphics aren't displaying, it's that freeview won't load because qt 
can't be initialized. Abeoseh FlemisterFrom: fsbuild 
<fsbu...@contbay.com>Sent: Friday, January 5, 2024 8:27 
PMTo: freesurfer@nmr.mgh.harvard.edu 
<freesurfer@nmr.mgh.harvard.edu>Cc: Flemister, Abeoseh B. 
<flemist...@missouri.edu>Subject: Re: [Freesurfer] recon-all -s 
SiroSTC006_pre exited with ERRORS  For issues with Freeview 
displaying graphics when running via Linux on a Windows host thru WSL, you 
could look at the recent thread with the subject "Re: [Freesurfer] Freeview not 
showing 
output", https://secure-web.cisco.com/1oaJ0JSPhxlRjzZbZiQ7yaftYm3TvYL5vsUqSvRIwn1mxTLB9TJXbethBhfapiwejmtZvkPk-Rzn2z_ad008-CzQlNve-NK6CceUt0VtPPFJdwtHKP55BXcuQhcU1YMz4-FPp9GzSTpiJ3JHu0iWTdbP786ULqlSTxSVgPgP7VkSxFmOR08R6XsMAhtGAScfuIli7yeGgO6_pGTXQjtPhYf_rpwzgCC2fxaK-4G43kajshNd4Ud6bVNH54fIM-6dcft-18wReIbRAerhMZzSx7hql2Jiwn18OCmUKqAcP8rn9FrqtaYOtu1LGeBs5QWaxiqN9ZGDiVySHjpAlv-EeZg/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg76229.htmlIn
 case the link to the Freesurfer WIKI talking about WSL is garbled in the URL 
above, that link 
is,https://secure-web.cisco.com/1EiWtVy6tBY8avsFO7RwETRF3_M-X-xF2Kpa7qQsUO9MBq9hJVTqFCn_eb9DM39rNtk3pbFG-ug4ZpEKk6X5eQ2KDMDYdDUh5TpmffuF5wXtAdJ4hB-SoNLiV1Eby6E2JQ7J-CCBMpK3-i117c1ChJq3VJ47f5OEtaSJW1rpGX1NRsG3fz4fL7KgiZcAesTpPNIIbOF0oVPc7kQgLZgqih4rx94xTA9NBpzpd1HjHFBdtCE_iQGSw6wkenZH9UDB92x5b8fE-xVb2Lshe0GJ8hZ4FWXijzgb14x-T7Jq75dJgbZtGXjWNynrOPhOFqkTqD0jXb80ORfn3PZQGWxIN5g/https%3A%2F%2Ffreesurfer.net%2Ffswiki%2FFS7_wsl_ubuntu-
 R.On Jan 5, 2024, at 21:08, Flemister, Abeoseh B. 
<flemist...@missouri.edu> 
wrote:External Email - Use 
CautionHi Yujing,Thanks 
that helped! I was trying to open freeview by typing "freeview" and I’ve 
unfortunately run into another error: This application failed to start 
because no Qt platform plugin could be initialized.I saw an email on 
this topic but I don't think it was ever answered.. Apologies if I'm reading 
the thread wrong. Any help would be greatly appreciated!Abeoseh 
FlemisterFrom: freesurfer-boun...@nmr.mgh.harvard.edu 
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Huang, Yujing 
<yhuan...@mgh.harvard.edu>Sent: Friday, January 5, 2024 3:05 
PMTo: Freesurfer support list 
<freesurfer@nmr.mgh.harvard.edu>Subject: Re: [Freesurfer] recon-all 
-s SiroSTC006_pre exited with ERRORS WARNING: This message has 
originated from an External Source. This may be a phishing expedition that can 
result in unauthorized access to our IT System.. Please use proper judgment and 
caution when opening attachments, clicking links, or responding to this 
email.This is from your recon-all.log“mri_convert 
/home/abeoseh/Downloads/OneDrive_1_1-4-2024/Subject 
6/Baseline/3D_T1_MPRAGE_PRE_MPR_AX.nii.gz 
/usr/local/freesurfer/subjects/SiroSTC006_pre/mri/orig/001.mgz mri_convert:
 extra argument 
("/usr/local/freesurfer/subjects/SiroSTC006_pre/mri/orig/001.mgz")“ There 
is a space in your path to nii.gz. Can you remove the space by renaming the 
directory? Also, your SUBJECTS_DIR points to your Freesurfer install 
directory - /usr/local/freesurfer/subjects. You might run into permission or 
symbolic link problems later. It is a good idea to set SUBJECTS_DIR to some 
other directory where you have write 
permissions. Best, Yujing From: freesurfer-boun...@nmr.mgh.harvard.edu
 <freesurfer-boun...@nmr.mgh.harvard.edu> On Behalf 
Of Flemister, Abeoseh B.Sent: Friday, January 5, 2024 3:31 
PMTo: freesur...@nmr.mgh.harvard.eduSubject: [Freesurfer] recon-all 
-s SiroSTC006_pre exited with 
ERRORS External Email - 
Use CautionHi FreeSurfer 
Team, I am attempting to run recon-all on a 3T MRI image dataset. I used 
recon-all \ -all \ -i 3D_T1_MPRAGE_PRE_MPR_AX.nii.gz \ -s SiroSTC006_pre and 
recon-all failed before completeing even the first step. I tried other files 
from our dataset and using .nii files and got the same result. I saw a 
recent thread where someone's issue was improperly labeled WM lesions but 
my dataset is composed of healthy brains.  I attached my 
reco

Re: [Freesurfer] recon-all -s SiroSTC006_pre exited with ERRORS

2024-01-05 Thread fsbuild

External Email - Use Caution

 For issues with Freeview displaying graphics when running via Linux on a 
Windows host thru WSL, you could look at the recent thread with the subject 
"Re: [Freesurfer] Freeview not showing output", 
https://secure-web.cisco.com/1_xzs3l0H18glGmrIaq7DLLWEnbalu4hRqRVJfIOVshijKYxcPt7YgAHaWtbElTSVhOHSVpXfVbYtsSat-VSB2AcASMfIu3iGWkg1Pr8PAWGiO-QNx_InTSbPx1SlEgEfWwHcu8Kvv6mpvP1DVjjMjrQm_tjS5mLYrxRY4oBZ9ZDYVcOJOgqZ1aNMNRZciur7DWeYIOQvMB3gIzoQ9Ezl_HmMYDUiQFPkcPHCm-jCkc9CwpFyswcD9oucICvpa2CcnjmJ_uKvLTTH3CMRECLNaxrDHkc_YoVNzJt4G1azbIURdLSwwIWcNW_J2fArM_PkVmgAJrH_G5HaO6Udtvukdw/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg76229.html
In case the link to the Freesurfer WIKI talking about WSL is garbled in the URL 
above, that link is,
https://secure-web.cisco.com/1NIeWPFmWL9ULg_YLAREetdCKnwA4CAjtUSmmia-2fJLaumxUt7nyh4UJA8ETOUN9ZoOiTX5WwcajQ_sDAOOVJakF-Aqee8hi58icmc6NHSfROyRiZ5TQY-ecyB2kKnjaz0f3e5_Qg6RK-x6-rP_zvRBzKHU2gEyZgr8ivRTUzaCtcYqTpgdC7euLsajGvu0lgP3hQGs-pjDgQFqARk41W-gp9vVlFfkqZ7jqrzUHbXKJSgVrIz7OvWhnctAqDmu7vpLk74tAGnyrzsoRpHRX9TuybAZMwjHHOKh7_IVpBAwPkmQXb9UMnyrtgutVQ871ASnKlGXL3HfgSgCUITnwMA/https%3A%2F%2Ffreesurfer.net%2Ffswiki%2FFS7_wsl_ubuntu
- R.
On Jan 5, 2024, at 21:08, Flemister, Abeoseh B.  
wrote:External Email - Use 
CautionHi Yujing,Thanks 
that helped! I was trying to open freeview by typing "freeview" and I’ve 
unfortunately run into another error: This application failed to start 
because no Qt platform plugin could be initialized.I saw an email on 
this topic but I don't think it was ever answered. Apologies if I'm reading the 
thread wrong. Any help would be greatly appreciated!Abeoseh 
FlemisterFrom: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Huang, Yujing 
Sent: Friday, January 5, 2024 3:05 
PMTo: Freesurfer support list 
Subject: Re: [Freesurfer] recon-all 
-s SiroSTC006_pre exited with ERRORS WARNING: This message has 
originated from an External Source. This may be a phishing expedition that can 
result in unauthorized access to our IT System. Please use proper judgment and 
caution when opening attachments, clicking links, or responding to this 
email.This is from your recon-all.log“mri_convert 
/home/abeoseh/Downloads/OneDrive_1_1-4-2024/Subject 
6/Baseline/3D_T1_MPRAGE_PRE_MPR_AX.nii.gz 
/usr/local/freesurfer/subjects/SiroSTC006_pre/mri/orig/001.mgz mri_convert:
 extra argument 
("/usr/local/freesurfer/subjects/SiroSTC006_pre/mri/orig/001.mgz")“ There 
is a space in your path to nii.gz. Can you remove the space by renaming the 
directory? Also, your SUBJECTS_DIR points to your Freesurfer install 
directory - /usr/local/freesurfer/subjects. You might run into permission or 
symbolic link problems later. It is a good idea to set SUBJECTS_DIR to some 
other directory where you have write 
permissions. Best, Yujing From: freesurfer-boun...@nmr.mgh.harvard.edu
  On Behalf 
Of Flemister, Abeoseh B.Sent: Friday, January 5, 2024 3:31 
PMTo: freesur...@nmr.mgh.harvard.eduSubject: [Freesurfer] recon-all 
-s SiroSTC006_pre exited with 
ERRORS External Email - 
Use CautionHi FreeSurfer 
Team, I am attempting to run recon-all on a 3T MRI image dataset. I used 
recon-all \ -all \ -i 3D_T1_MPRAGE_PRE_MPR_AX.nii.gz \ -s SiroSTC006_pre and 
recon-all failed before completeing even the first step. I tried other files 
from our dataset and using .nii files and got the same result. I saw a 
recent thread where someone's issue was improperly labeled WM lesions but 
my dataset is composed of healthy brains.  I attached my 
recon-all..logs. I am using a Linux virtual machine (FreeSurfer version 
freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460). Please let me know if 
you have any questions! Thanks,Abeoseh 
Flemister___Freesurfer mailing 
listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail.

Re: [Freesurfer] Freeview not showing output

2024-01-04 Thread fsbuild

External Email - Use Caution

As Ruopeng said, even if simple X-Windows programs like glxgears run, that does 
not mean freeview will display graphics.
If freeview is not displaying images after X-ming (or a different) 
 X-Windows server runs on the Windows host and displays graphics from 
glxgears, then there is likely something not right with the OpenGL drivers 
working with the graphics hardware on the Windows host.  Usually the fix 
is to update to the latest OpenGL drivers on the Windows host.
If you have not read through or tried the steps on this Wiki page, then it 
might help,  
https://secure-web.cisco.com/12p37USRW5-RyLF2YXnbTAoizwyX5lHFSny043woIbJwaVA1Q6_A8YJxMdsz083PotIEQxfNhBetezn8unJ3bpT7arlesM-opVIvQ-jxqHg6UZaTwwFvbkIbzmvXhlHlC02MgLrOwtH-BShA0LaKafUr8T7AWZt5Dy1bKLSpvXObbJNND8nFFzU6ikjAOYv8JvCwMSODydsxNuBgPbsqak7GwjQ3Ap4BqUrQHcZN4UX_4jgm1-o9L_odJwgkN4z7eGgHh9wg2zsdJrbBiJSkETQeqnnIC58Lc8iamkihm7PokgUoRcCHqiEG0hpPWCb2tqimgLM9hYepeAUqcX8FTtA/https%3A%2F%2Ffreesurfer..net%2Ffswiki%2FFS7_wsl_ubuntu
If you are seeing graphics from glxgears then I would presume DISPLAY and 
XDG_RUNTIME_DIR are likely set OK in Linux.
- R.

On Jan 4, 2024, at 10:08, Wang, Ruopeng  wrote:It 
appears your system has some problem displaying OpenGL content properly. I’m 
not familiar with Xming. Can you try some other x display for Windows such as 
mobaxterm?https://secure-web.cisco.com/1KYKTifNL0XRk6k_SapoZX6CTHF_pDgzD6UKF0dkksoSBoqImuAD98rrLboBd_aYWt93uiZcob83wd88Crd8E4w6HbvVkhUVwS-CFa__hpvt-RsRpD40l9EbM2nCjm3OlP-ailtdAw2JpkXjxXQiLyTFabILi3agYXU2Jlj8KQ8U1mG56Pnrzu9EGa4BgFUvqu5fXNHC8JzXAm3Ktv-7W5FqCSV4yvg0ORKm7Jgt5fCYUzzQCBTvCdkJPxlX0KCk8gXd6N4W0BXKiNpFFX1N-2zy1vKf80kre0reP_cD6emR7ZsP_67hH_apBmofRuDaMT7PpM1pYGe2F2WunI4xJgw/https%3A%2F%2Fmobaxterm.mobatek.net%2FOn
 Jan 4, 2024, at 6:11 AM, Shawa, Zeena  
wrote:External Email - Use 
CautionHi Ruopeng, Thank 
you for your quick reply!When running glxgears I just see a blank 
window. Sincerely,Zeena 
Shawa From: freesurfer-boun...@nmr.mgh.harvard.edu  On
 Behalf Of Wang, RuopengSent: Wednesday, January 3, 2024 4:29 
PMTo: Freesurfer support list 
Subject: Re: [Freesurfer] Freeview 
not showing output ⚠ Caution: External sender What if you run 
glxgears command? Do you see 3D spinning gears or just a blank 
window? RuopengFrom: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Shawa, Zeena 
Sent: Wednesday, January 3, 2024 9:17:00 
AMTo: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer]
 Freeview not showing 
output External Email - 
Use CautionHello FreeSurfer 
Developers and Community, Hope your day has been going well and happy new 
year! I'm attempting to visualise FreeSurfer outputs using freeview, as 
described on the “Introduction to Freesurfer Output” tutorial, under the 
“Viewing Volumes with Freeview” section (MailScanner has detected a possible 
fraud attempt from "secure-web.cisco.com" claiming to 
be https://secure-web.cisco.com/1wzX4cge9MlMx5r_8jnAVeO8ue9DOKEESG6wS-RZbEzhXP-7pQaQgxBK8QyBF7hm-bqYBz_sBcNzsM9MxEQ-owoVqQmRLE8GKpOudIwJavI3EU6YF_Bs_uAcZfSLu7O8gR4W_mzt643W0rot3Z4yPSTE3IePMTVkJV27B2yH3OF6BwcPOoP1ZfXocrxR56_ANZV8XjyeQaOQ5D9BY7BRh1gcp_P57Orpb9r_0CgjBkFDZL9nBqKcNgdmgbNshaYmrvP5yk_fMjqkC87ych1b9nPkqMBOnxpXESn_d39nq6tSxFAIGSpeutQYRT9L5CNGoL4z5e5xLi2rNrI0cDiXNCA/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsTutorial%2FOutputData_freeview%26nbsp;).
 The viewer launches fine and seems to load everything, but instead of showing 
any output it simply shows a black screen in the middle (screenshot attached). 
There is no error outputted in the command line either. The viewer seems to 
work fine otherwise, and I have completed the Xming X-server setup as described 
here: MailScanner has detected a possible fraud attempt from 
"secure-web.cisco.com" claiming to 
be https://secure-web.cisco.com/18qHMAU0T79b7NwnKw9Zpf5tUXLvkF9EnPH2_5X4-JibgPev_yLgH9bOmnOl9ki6tsL6KJAPJ89TBivch0oRDHLcHX9p2zemlApVOavfNMc-oVeLvXDLYMfg46MM5nK0UOFATMr9pJhI1-RGWNYv073vMPVhYUMtVYo0_C8Rdgsw4Fz5Pd9NcVLJBUFY7uHP2NMrO9f7Hj201yg7U7OmezaP47vYHFgVw_Um1LN2zKYmYZZtbOoGyxl--WMOdEZ6YE9BbwFADgcB6KRW3UVvjR55-8xnv8jsDNhhNH1cBrcEZPSpsUs6gxuHuJtDcu7LTvHS_ZIUJ7xLZjI51NjzLnQ/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFSL_wsl_xming%26nbsp;. I've
 searched the archives and GitHub issues and cannot find a similar error. I 
would appreciate any feedback on how to troubleshoot this issue.Thank you very 
much for your understanding and help!  FreeSurfer version: 
freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460Freeview 
version: Version 3.0, June 14 2023 buildXming versions: Xming fonts 
7.7.0.10, Xming 6.9.0.31Platform: WSL2 Ubuntu 22.04.3 LTSuname -a: Linux 
LAPTOP-4153LQMG 5.15.133.1-microsoft-standard-WSL2 #1 SMP Thu

Re: [Freesurfer] Help (Freeview fails to launch)

2023-12-29 Thread fsbuild

External Email - Use Caution

Depending upon the state of a machine, there is no guarantee a list of 
"required" packages will encompass everything that needs to be 
installed/updated, or that a manual install will work.  So we neither 
recommend or support manual/piecemal installs, e.g., via the list below, 
instead of using the built-in linux package management tools.

- R.

On Dec 29, 2023, at 22:32, Kiyotaka Nemoto <kiyot...@nemotos.net> 
wrote:External Email - Use 
CautionDear Akira,I agree with 
R that installing FreeSurfer using the deb is preferred, but if you want 
to stick to tar.gz,below is the list of the packages to be installed when you 
install FreeSurfer using the deb package.So if you install these packages, you 
would be able to run freeview.Hope this helps,Kiyotakasudo apt install -y 
language-pack-en binutils libx11-dev gettext x11-apps \  perl make csh 
tcsh bash file bc gzip tar \  xorg xorg-dev xserver-xorg-video-intel 
libncurses5 libbsd0 libc6 libc6 \  libcom-err2 libcrypt1 libdrm2 libegl1 
libexpat1 libffi7 libfontconfig1 \  libfreetype6 libgcc-s1 libgl1 
libglib2.0-0 libglu1-mesa libglvnd0 libglx0 \  libgomp1 libgssapi-krb5-2 
libice6 libjpeg62 libk5crypto3 libkeyutils1 \  libkrb5-3 libkrb5support0 
libpcre3 libpng16-16 libquadmath0 libsm6 \  libstdc++6 libuuid1 
libwayland-client0 libwayland-cursor0 libx11-6 \  libx11-xcb1 libxau6 
libxcb-icccm4 libxcb-image0 libxcb-keysyms1 \  libxcb-randr0 
libxcb-render-util0 libxcb-render0 libxcb-shape0 \  libxcb-shm0 
libxcb-sync1 libxcb-util1 libxcb-xfixes0 libxcb-xinerama0 \  
libxcb-xinput0 libxcb-xkb1 libxcb1 libxdmcp6 libxext6 libxft2 libxi6 \  
libxkbcommon-x11-0 libxkbcommon0 libxmu6 libxrender1 libxss1 libxt6 
zlib1g  On Fri, Dec 29, 2023 at 12:14 PM fsbuild 
<fsbu...@contbay.com> 
wrote:External Email - Use 
Caution That message could 
be the result of missing system libraries which the Ubuntu 22 FS 7.4.1 .deb 
package will try to automatically identify, download and install for you.  
You can download the package via the link MailScanner has detected a 
possible fraud attempt from "secure-web.cisco.com" claiming to 
behttps://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/7.4.1/freesurfer_ubuntu22-7.4.1_amd64.deb and
 the install can be done with,… cd to your Downloads to wherever the .deb file 
is …$ sudo apt install  ./freesurfer_ubuntu22-7.4.1_amd64.debIf the 
install succeeds, freesurfer will be under /usr/local/freesurfer/7.4.1 which is 
the path to use for the environment variable FREESURFER_HOME,$ export 
FREESURFER_HOME=/usr/local/freesurfer/7.4.1If they are not already set in your 
environment, you should also set,$ export XDG_RUNTIME_DIR=$HOME/.xdg$ 
export DISPLAY=:0- R.On Dec 27, 2023, at 23:17, Akira Kita 
<jorrydep9...@gmail.com> 
wrote:External Email - Use 
CautionI have installed 
FreeSurfer 7.4.1 on Ubuntu 22.04 using the binary tar archive 
freesurfer-linux-ubuntu22_amd64-7.4.1.tar.gz.Freeview fails to launch with the 
following error message:This application failed to start because no Qt platform 
plugin could be initialized. Reinstalling the application may fix this 
problem.  Available platform plugins are: eglfs, linuxfb, minimal, 
minimalegl, offscreen, vnc, wayland-egl, wayland, webgl,How can I solve 
this?　　　Akira___Freesurfer mailing 
listfreesur...@nmr.mgh.harvard.eduMailScanner has detected a possible fraud 
attempt from "secure-web.cisco.com" claiming to 
behttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer___Freesurfer
 mailing listfreesur...@nmr.mgh.harvard.eduMailScanner has detected a possible 
fraud attempt from "secure-web..cisco.com" claiming to 
behttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer-- Kiyotaka 
Nemoto, M.D., Ph.D.Associate ProfessorDepartment of PsychiatryDivision of 
Clinical Medicine, Institute of MedicineUniversity of Tsukuba1-1-1 Tennodai 
Tsukuba, Ibaraki 305-8575, 
JapanE-mail: kiyotaka@nemotos.net___Freesurfer
 mailing 
listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] Help (Freeview fails to launch)

2023-12-28 Thread fsbuild

External Email - Use Caution

 That message could be the result of missing system libraries which the 
Ubuntu 22 FS 7.4.1 .deb package will try to automatically identify, download 
and install for you.  You can download the package via the 
link https://secure-web.cisco.com/1t9e2mCgXLQVxO1_HRQVcGKF8xT7sodKwA6zzWD3PnvYpEYhzi545ja6T6zaKK2EKrLVHMv6-PenWRMiweIekDa0iPsOeO98ft16CafenUS7q9BCgUBIUTZ4DVfUj_bzh0uPOyWvS4HQa596zdcqA4rd_Q-K_M2WisVZhilBIGDxBi6g1no1JAF0xGe8QRbw1_MNpA42GJvTyE3Ps_fzXnMymgErLwVj6rpub0SX6CnI2T2f2hJ-5kA2_45a9Cuj-xUsFMqWPuXjSNYYpq3gSvNU9KSI_nj_yxnrBbLWqZOIW4xjT17yKPejFlXKp808Nd2U_ZOe-9oEV5ZotlsGDQw/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Fpub%2Fdist%2Ffreesurfer%2F7.4.1%2Ffreesurfer_ubuntu22-7.4.1_amd64.deb%26nbsp;and
 the install can be done with,
… cd to your Downloads to wherever the .deb file is …
$ sudo apt install  ./freesurfer_ubuntu22-7.4.1_amd64.deb
If the install succeeds, freesurfer will be under /usr/local/freesurfer/7.4.1 
which is the path to use for the environment variable FREESURFER_HOME,
$ export FREESURFER_HOME=/usr/local/freesurfer/7.4.1
If they are not already set in your environment, you should also set,
$ export XDG_RUNTIME_DIR=$HOME/.xdg
$ export DISPLAY=:0

- R.

On Dec 27, 2023, at 23:17, Akira Kita  
wrote:External Email - Use 
CautionI have installed 
FreeSurfer 7.4.1 on Ubuntu 22.04 using the binary tar archive 
freesurfer-linux-ubuntu22_amd64-7.4.1.tar.gz.Freeview fails to launch with the 
following error message:This application failed to start because no Qt platform 
plugin could be initialized. Reinstalling the application may fix this 
problem.  Available platform plugins are: eglfs, linuxfb, minimal, 
minimalegl, offscreen, vnc, wayland-egl, wayland, webgl,How can I solve 
this?　　　Akira___Freesurfer mailing 
listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] segmentBS.sh not found

2023-12-26 Thread fsbuild

External Email - Use Caution

 On linux, that file is under $FREESURFER_HOME/bin and will be found in 
your PATH after you setup the Freesurfer environment, e.g. for the 7.2.0 
release installed via the .rpm file, you setup the environment with,
$ export FREESURFER_HOME=/usr/local/freesurfer/7.2.0-1
$ source $FREESURFER_HOME/SetUpFreeSurfer.sh
 freesurfer-linux-centos7_x86_64-7.2.0-20210720-aa8f76b 
Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME   /usr/local/freesurfer/7.2.0-1
FSFAST_HOME       /usr/local/freesurfer/7.2.0-1/fsfast
FSF_OUTPUT_FORMAT nii.gz
SUBJECTS_DIR      /usr/local/freesurfer/7.2.0-1/subjects
MNI_DIR         
  /usr/local/freesurfer/7.2.0-1/mni
$ which segmentBS.sh
/usr/local/freesurfer/7.2.0-1/bin/segmentBS.sh
$ segmentBS.sh -h
     ERROR: cannot find Matlab 2014b runtime in location:
     /usr/local/freesurfer/7.2.0-1/MCRv84… rest of output 
deleted ..
So if you have not already installed the MATLAB runtime environment for 
the segmentBS.sh script, then you need to run the Matlab install script we 
provide.  For the Freesurfer install under /usr/local on linux, the Matlab 
install needs to be done with root/admin privileges which you can try via the 
sudo option,
$ cd $FREESURFER_HOME/bin$ sudo  FREESURFER_HOME=$FREESURFER_HOME 
 ./fs_install_mcr  R2014b
… you will see output from downloading and installing the matlab runtime under 
/usr/local/freesurfer/7.2.0-1/MCRv84 …You should follow the instructions from 
the script output about how to set LD_LIBRARY_PATH, e.g.,
On the target computer, append the following to your LD_LIBRARY_PATH 
environment variable:
/tmp/tmp.e23XcWLTeV/install-target/v84/runtime/glnxa64:/tmp/tmp.e23XcWLTeV/install-target/v84/bin/glnxa64:/tmp/tmp.e23XcWLTeV/install-target/v84/sys/os/glnxa64:
Your paths may be different, but you would modify the LD_LIBRARY_PATH setting 
as follows; I just cut and pasted the /tmp/* paths anover after "export 
LD_LIBRARY_PATH=$LD_LIBRARY_PATH:”,
$ export 
LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/tmp/tmp.e23XcWLTeV/install-target/v84/runtime/glnxa64:/tmp/tmp.e23XcWLTeV/install-target/v84/bin/glnxa64:/tmp/tmp.e23XcWLTeV/install-target/v84/sys/os/glnxa64
You could follow the same instructions as listed above for the 7.4.0 release, 
i.e.. change 7.2.0 to 7.4.0 in all the commands (and corresponding output 
should list 7.4.0 instead).  The segmentBS.sh in 7.4.0 might ask for a 
newer Matlab version like MCRv97.   In that case, the sudo command to run 
the fs_install_mcr script would be,$ sudo 
 FREESURFER_HOME=$FREESURFER_HOME  ./fs_install_mcr  R2019b
Once Matlab runtime is installed, try running segmentBS.sh again,
$ segmentBS.sh -h
 Directory of subject to process:
   /usr/local/freesurfer/7.2.0-1/subjects/-h
does not exist
So change SUBJECTS_DIR to the path containing the subject data you want to 
process,
$ export SUBJECTS_DIR=/path/to/my/subjects
… then try running again ...

- R.

On Dec 26, 2023, at 19:32, Ganjizadeh, Ali, M.D. 
 wrote:segmentBS.sh

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] Freesurfer/Freeview Version Compatibility

2023-12-20 Thread fsbuild

External Email - Use Caution

The freesurfer 6.X and 7.x release release notes summarize some changes for
Freeview (listed below) since version 5 was released in 2013. If none of
the improvements in features/stability are relevant to what you are doing, then
I don’t see why you could not revert to the older 5.X software. But if
you run into issues with a now ~10 year old version of Freeview, we may tell
you to use the latest 7.4.1 release from June of 2023.
- R.
- - - - -

• New: interface for x virtual frame buffer (fsxvfb). When you run
freeview from fsxvfb, no X server is needed. This is good for taking a bunch of
pictures when you don't want freeview popping up all the time. Eg, fsxvfb
freeview orig.mgz -ss mypic.png —quit
• The filled.mgz can now be edited instead of the wm.mgz. The
advantage to this is that filled.mgz is slightly further in the process and it
is more intuitive. The filled.mgz is actually a segmentation of the
subcortical mass. In Freeview, you can view it in outline mode, meaning that
the edges of the segmentations are actually the surface that you are editing.
After that, run recon-all with the -autorecon2-wm -autorecon3 options, just as
you would if you had edited the wm.mgz..Landmark-based repositioning of
surfaces. Did you ever want to just make the surface move through a certain
point? You can do that now by creating point sets in freeview. Create a
separate point set for each surface (lh, rh, white, and pial), then save it in
subject/surf with a file name repos.$hemi.$surf.json where $hemi is either lh
or rh and $surf is either white or pial. Then run recon-all with the
-autorecon2-surfonly -autorecon3 options. Note that you can do this
interactively inside of FreeView as well; look under
Tools->Resposition Surface. If you do it interactively, the surface may be
overwritten next time recon-all is re-run, but it gives you a chance to play
with the repositioning.freeview - can now load and visualize diffusion
orientation distribution function (ODF) data.FreeView changes: surfce path
and label editing, surface annotation editing, automatic segmentation assisted
by Geodesic Matting algorithm, displaying two time courses at the same time,
better support for Mac (petsc error fixed on Mac)

On Dec 20, 2023, at 14:07, Edwards, Vincent

wrote:External Email - Use
CautionHi, I'm following
up on my quick question from this time last week. I have several brains
that I sent through recon-all using Freesurfer 7. If I wanted to use Freeview
on Freesurfer version 5 to do pial/wm/and control point edits, would I be able
to do recon-all through Freesurfer 7? Years ago, someone asked if they
could do recon-all in an older version of Freesurfer and edit in a newer GUI.
Doug said that was fine. My question is basically the inverse of their
problem. I assumed that since Freeview is a GUI, the version used
shouldn't have any actual impact on things as long as we returned to version 7
to recon-all. I just want to confirm that my assumption is correct?The
pipeline would be: F7 (recon-all), F5 (edit with freeview), F7 (recon-all
for pial/wm/cp's)Thanks,Vincent
Edwards___Freesurfer mailing
listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] Longitudinal LME matlab error - Matrix singular or badly scaled

2023-12-11 Thread fsbuild

External Email - Use Caution

I don’t think there is any GUI or graphical interface with the runtime 
environment (which does not require a Matlab license).  Neither does it 
contain the matlab compiler to build matlab executables, etc.  So if you 
still need to create Matlab executables either with the GUI or from the command 
line, you would need to have your own site or personal installation of Matlab 
with a license.  The Matlab runtime environment in freesurfer subsequently 
allows you to run what has already been built with Matlab.
- R.

On Dec 10, 2023, at 21:31, Sophie Matis  
wrote:External Email - Use 
CautionHi there, Thanks 
for the advice, I have followed these suggestions and used the fs_install_mcr 
command and can see the the libmwm* libraries are installed under 
$FREESURFER_HOME/MCRv97/bin/glnxa64. I also added the path the script suggested 
once finished to LD_LIBRARY_PATH. I’m now not sure how to open matlab now 
though as I can’t find any executable matlab file? There were no error with the 
command but it doesn’t look like matlab was installed… Thanks again for 
the help, Sophie Matis | Data Management & Research OfficerSchool 
of Health Sciences & Brain and Mind Centre Faculty of Medicine and 
Health  The University of Sydney  Brain and Mind Centre, 
94-100 Mallett Street, Camperdown (M02G) | The University of Sydney | NSW 
| 2006 sophie.ma...@sydney.edu.au  | sydney.edu.au CRICOS 
00026AThis email plus any attachments to it are confidential. Any unauthorised 
use is strictly prohibited. If you receive this email in error, please delete 
it and any attachments. Please think of our environment and only print 
this email if 
necessary. From: freesurfer-boun...@nmr.mgh.harvard.edu  On
 Behalf Of fsbuildSent: Saturday, November 25, 2023 6:43 
AMTo: freesur...@nmr.mgh.harvard.eduSubject: Re: [Freesurfer] 
Longitudinal LME matlab error - Matrix singular or badly 
scaled External Email - 
Use Caution Hello 
Sophie,Just FYI, there is no matlab distribution included in the 7.4.1 release 
and we so not support using R2023b.  So I presume someone at your site 
installed R2023b separately via a Mathworks matlab installer.  We do 
provide a script, fs_install_mcr, to install either the R2014b or R2019b matlab 
runtime environment into the freesurfer tree for use.  I don't know if 
running R2019b would affect what you report below, but you could try it via the 
commands below.- R.$ export 
FREESURFER_HOME=/usr/local/freesurfer/7.4.1 
 <--- linux install path$ source $FREESURFER_HOME/SetUpFreeSurfer.sh<... 
output showing SUBJECTS_DIR and other environment variables>$ cd 
 $FREESURFER_HOME/bin$ sudo FREESURFER_HOME=$FREESURFER_HOME 
 ./fs_install_mcr  R2019bI believe this sets things up so the libmwm* 
libraries are installed under $FREESURFER_HOME/MCRv97/bin/glnxa64.  You 
can try adding that path (or any path the script output recommends) to the 
start of LD_LIBRARY_PATH.  You should remove any other entries to a 
different MATLAB distribution.On 11/23/23 20:42, Sophie Matis 
(sophie.ma...@sydney.edu.au) 
wrote:External Email - Use 
CautionHello FreeSurfer 
experts! I have carried out some analysis of changes in cortical thickness 
over time using the LME Matlab (R23b) Toolbox distributed within Freesurfer 
(7.4.1) in line with the instructions on this page:  MailScanner has 
detected a possible fraud attempt from "secure-web.cisco.com" claiming to 
behttps://surfer.nmr.mgh.harvard.edu/fswiki/LinearMixedEffectsModels At 
this stage I just want to look at changes over time within each of three 
groups. For two groups I have been able to proceed through the steps fine and 
have my significance files which look normal. For the last group I am running 
into an error on the “[lhTh0,lhRe] = lme_mass_fit_EMinit(X,[1 
2],Y,ni,lhcortex,3); “ step. MATLAB returns “Warning: Matrix is singular, close 
to singular or badly scaled” and lhTh0 and lhRe are created as matrices with 
only NaN values.  Has anyone run into this error before or have any 
tips for troubleshooting it? I haven’t had any errors on the longitudinal 
processing steps and visual QC on my files looks normal. No errors on 
mris_preproc or mri_surf2surf.  An aparcstats2table for thickness doesn’t 
reveal any NaNs.  My design matrix is created with X = 
[ones(length(M),1) M] after following the suggested sortData code from the 
wikiContrast is [0 1]This is my qdec file: fsid    
fsid-base   
yearsfromBL108_MR1   108   
0.00199_MR1   199   
0.00199_MR2   199   
1.10199_MR3   199   
2.25202_MR1   202   
0.00204_MR1   204   
0.00204_MR2   204   
1.16204_MR3   204   
2.30223_MR1   223   
0.000821_MR1  0821  
0.000931_MR1  0931  
0.001010_MR1  1010  
0.001010_MR2  1010  
1.841031_MR1  1031  
0..001031_MR2  1031  
1.001031_MR3  1031  
2.1

Re: [Freesurfer] FreeSurfer release for Redhat Linux 9.x and its clones

2023-12-11 Thread fsbuild

External Email - Use Caution

We hope to have a binary rpm installer for CentOS9.
I have not tried it, but the existing FS 7.4.1 CentOS8 binary rpm installer 
(https://secure-web.cisco.com/1mIKM9a0zhqsi_mcRwphvOt3o7Sjq5psvoHs9PCYVk-9pm31XnoNmc3uba-p0gcATG3DclmaBNOQlLGbQfbntyqmIFwtlf_Gu14HSDaAKMr0K2yeT5F8huY5-algIEf1xrr93MTyZcmApf_zFVYBqtDhy2IBQw1YyyGTijcU0hXXpzH_zypUF9sttXAJSRLW-PPd8vMTssdt4mBfHyH-gANEwifN4bAMHMc9sLUXZ8h5fyOKChUBtPaU3VMOODOFGToEX5X1ZpCrFkMxCptfhhGT6Mcaxt8ZJSl9FKmpBdFo6vWQsYSsXQe8yfgqxL8FUC7D8jkaZzMktzoyRaefM-Q/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Fpub%2Fdist%2Ffreesurfer%2F7.4.1%2Ffreesurfer-CentOS8-7.4.1-1.x86_64.rpm)
 might already install on RedHat/CentOS 9.
- R.

On Dec 11, 2023, at 11:16, Li, Mingyi  
wrote:External Email - Use 
CautionWill there be a binary 
release of FreeSurfer for Redhat Linux 9.x clones such like Rocky Linux 9.x or 
Oracle Linux 
9.x? Thanks, Mingyi   Mingyi Li, 
Ph.D.  |  Director of Scientific Computing  |  Imaging 
Institute  9500 Euclid Ave. |  Cleveland, OH 44195 | 
216-444-8112, 216-401-8585   Please consider the environment 
before printing this e-mailCleveland Clinic is a nonprofit, multispecialty 
academic medical center that's recognized in the U.S. and throughout the world 
for its expertise and care. Visit us online at MailScanner has detected a 
possible fraud attempt from "secure-web.cisco.com" claiming to 
be http://secure-web.cisco.com/1mdjBr0gnFKSPamS90gvnuVllKIajUVfySxtCx_7BlYGdlApDaw3kx6nu8gbiQEB1AEIsh_Y1eGdKUQ08lGLwaaiWaGJUl4nvGo_RqFIFyloq00LrnrnamajIpNcjw12QjGafPKVX69hdHhY77pYDJna6_pJN1HTKmRIMuhNPP3rglzXDyb_JJ3fWFQo4TbFGd9xpy98PDF2B1vx0sFly1AF1wahoXXCs47eJmvvwcHx-hQjf5sMKs5ZO-T8QkWXDtrfFHjYW_gAFL7jKQ7gqeaCABRJ3vrYw5791wFInKXOHeycQt5l1NW-OMkMLDsPaiE4Nmmu3VtvI_c7KenhKzg/http%3A%2F%2Fwww.clevelandclinic.org%26nbsp;for
 a complete listing of our services, staff and locations. Confidentiality Note: 
This message is intended for use only by the individual or entity to which it 
is addressed and may contain information that is privileged, confidential, and 
exempt from disclosure under applicable law. If the reader of this message is 
not the intended recipient or the employee or agent responsible for delivering 
the message to the intended recipient, you are hereby notified that any 
dissemination, distribution or copying of this communication is strictly 
prohibited. If you have received this communication in error, please contact 
the sender immediately and destroy the material in its entirety, whether 
electronic or hard copy. Thank you. 
___Freesurfer mailing 
listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] Issue with FreeSurfer on VirtualMachine

2023-12-11 Thread fsbuild

External Email - Use Caution

There’s no need to have a license file in a particular location if you set the 
environment variable FS_LICENSE to point to the license file.
If you are using the Ubuntu 18 VM made available with Freesurfer 7, then adding 
the license.txt file you received to developer’s home directory should have 
caused FS_LICENSE as set in the environment to read it,
$ cd $HOME$ pwd/home/developer$ ls -l license.txt… and you should see something 
like ...-rw-rw-r— 1 developer developer  nn  month  day 
 hours:minutes  license.txt$ echo 
$FS_LICENSE/home/developer/license.txt$ head -1  
$fs_license...@somewhere.com      <—— email you used to 
register
If the above is not working in your copy of the VM, then set FS_LICENSE 
manually,
$ export FS_LICENSE=/path_to_file/license.txt
- R.
On Dec 11, 2023, at 18:37, Fargol Rezayaraghi  
wrote:External Email - Use 
CautionDear FreeSurfer Team,I 
hope this email finds you well. I'm Fargol, a PhD candidate at the University 
of Washington. I followed your guidance to use FreeSurfer on the virtual 
machine successfully. I obtained the license as instructed.However, I faced two 
problems while trying to use FreeSurfer on VirtualMachine:I'm unable to move 
the license file to a different directory within VirtualMachine.Even when I 
attempt to add the license in a different directory, I receive an error message 
stating that I don't have permission to do so.Could you please assist me in 
resolving these issues so that I can utilize FreeSurfer effectively on 
VirtualBox?Thank you for your help in advance.Kind regards,Fargol-- Kind 
Regards,Fargol R. Araghi (Rezayaraghi)Ph.D. Candidate, University of 
WashingtonDepartment of Mechanical EngineeringMailScanner has detected a 
possible fraud attempt from "secure-web.cisco.com" claiming to 
be http://secure-web.cisco.com/1V9po0H9Hi_A721VJEJ_KCqT4Fl61Q3_VavajV-5Zlepm5ANo9pPC4U4LFKQ6UdR3k1UwBzZIv3Crte2Sanl5o-mm5zz0Q8VjK9Npv3zikvdEIR5-F8oLjX7e5Yr2tMDNKgz0WkoKIYgIo9GNnRJGQDPfBiBVZCU25eNnHI3hnT_PiumxN3biIJtygAAyaxp3emSC7kkExPTRxCvE7DEpOcSJceK1rGcaPxLORUbcizzsmDN7Ob4GEAOFZb5rCBEVVTBGSNPQs4Sj9ffSTtFrl2xZJC_7XaP1FVRCuxTb6lPa03DZtSriIQ-15-qwvQQKX_T1VN8buX2L6H9UQi64SA/http%3A%2F%2Fwww.Kurtlab.com___Freesurfer
 mailing 
listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] Freesurfer 7.3.1 MCR 2019b

2023-12-06 Thread fsbuild

External Email - Use Caution

 

I believe the assumption is the freesurfer 7.3.1 distribution has already
 been installed (under /usr/local/freesurfer/7.3.1 by the *.deb or *.rpm
 linux installer file) and that FREESURFER_HOME is set in the 
environment  (/usr/local/freesurfer/7.3.1).  You should be able to 
download and run the 7.3.1 freesurfer installer using one of the 7.3.1 
links from 
https://secure-web.cisco.com/1JcyAuFpIReuF1zXqp8tlLsd3XWfOZVJNAxAaV1v1-OILtBqSGQrYB9hxeZJmR16KxuOpIYEX4SyiD60s5b0YkTlJJpaEUBj6KXV2fiheUQ1TB1u0pxsL60cXvfV8Ys62qmwfMf-f-o7q-JM-YahLFX0T7553tGWCgbLRHT2qSqpKN0Al7eFTpKNFb0_h-wxPsYa4YldQ7j16UgeL1JxO0SVH3K8PRBjEg2nGBYcnp0e9ntYcTxsFwhkOODhvnlsk48-GxpBr5A4BSeBorxZ4b0cVUvqY3sUu9LqUFYn4G99x31v9evnPWeXcyOZrDQBp/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2Frel7downloads



After running the freesurfer installer, the steps - which it looks like 
you are already using - are listed below from a bash terminal window,



$ export FREESURFER_HOME=/usr/local/freesurfer/7.3.1



$ cd  $FREESURFER_HOME/bin



 you can try using either R2019b or R2014b ...



$ sudo FREESURFER_HOME=$FREESURFER_HOME  ./fs_install_mcr  R2019b



I'm not sure the paths generated by the Maltab installer for use in 
LD_LIBRARY_PATH are always the same.   They may not be if it uses 
some 
temporary path naming mechanism.  So you may need to capture
 the output from the matlab installer, parse out the LD_LIBRARY_PATH 
setting each time it is run, and set it in the environment.



- R.



On 12/6/23 13:58, Na, Xiaoxu (x...@uams.edu) wrote:







  External Email - Use 
Caution

  
Dear Freesurfer Experts,
 
I’m building a docker file with freesurfer and 
matlab run time. May I know if freesurfer 7.3.1 should be compatible 
with matlab run time 2019b?
If so, what else can I make the environment setting correct in order to run 
localGI?
 
I tried to run “cd $FREESURFER_HOME/bin && 
sudo FREESURFER_HOME=$FREESURFER_HOME ./fs_install_mcr R2019b” and it 
finished successfully and I also appended the 
“/opt/freesurfer-7.3.1/MCRv97/runtime/glnxa64:/opt/freesurfer-7.3.1/MCRv97/bin/glnxa64:/opt/freesurfer-7.3.1/MCRv97/sys/os/glnxa64:/opt/freesurfer-7.3.1/MCRv97/extern/bin/glnxa64:/opt/freesurfer-7.3.1/MCRv94/bin/glnxa64/libmwlaunchermain.so”
 to  "$LD_LIBRARY_PATH". 
 
On the target computer, append the following to your LD_LIBRARY_PATH 
environment variable:
 
/tmp/tmp.T0m3Pxj9fW/install-target/v97/runtime/glnxa64:/tmp/tmp.T0m3Pxj9fW/install-target/v97/bin/glnxa64:/tmp/tmp.T0m3Pxj9fW/install-target/v97/sys/os/glnxa64:/tmp/tmp.T0m3Pxj9fW/install-target/v97/extern/bin/glnxa64
 
If MATLAB Runtime is to be used with MATLAB Production Server, you do not need 
to modify the above environment variable.
 
(Dec 06, 2023 17:26:10) Exiting with status 0
(Dec 06, 2023 17:26:10) End - Successful.
Finished
R2019b installed successfully in /opt/freesurfer-7.3.1/MCRv97
Removing intermediate container afe25e3801f1
---> ae8788b3fa89
Step 13/14 : ENV 
LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/lib/x86_64-linux-gnu:/opt/freesurfer-7.3.1/MCRv97/runtime/glnxa64:/opt/freesurfer-7.3.1/MCRv97/bin/glnxa64:/opt/freesurfer-7.3.1/MCRv97/sys/os/glnxa64:/opt/freesurfer-7.3.1/MCRv97/extern/bin/glnxa64:/opt/freesurfer-7.3.1/MCRv94/bin/glnxa64/libmwlaunchermain.so
---> Running in e3601f8c33c4
Removing intermediate container e3601f8c33c4
---> 404199efd51a
Step 14/14 : RUN echo "$LD_LIBRARY_PATH"
---> Running in ac3754cb24bb
:/usr/lib/x86_64-linux-gnu:/opt/freesurfer-7.3.1/MCRv97/runtime/glnxa64:/opt/freesurfer-7.3.1/MCRv97/bin/glnxa64:/opt/freesurfer-7.3.1/MCRv97/sys/os/glnxa64:/opt/freesurfer-7.3.1/MCRv97/extern/bin/glnxa64:/opt/freesurfer-7.3.1/MCRv94/bin/glnxa64/libmwlaunchermain.so
Removing intermediate container ac3754cb24bb
---> 9e9c3e2e0051
Successfully built 9e9c3e2e0051
 
 
However, when I run “recon-all -s BL-101 -localGI” 
on the subject BL-101 that was successfully finished was recon-all 
previously, it yelled Malab was not available. Could you please help 
where I did wrong? Thank you so much!
 
start
/usr/lib/x86_64-linux-gnu:/opt/freesurfer-7.3.1/MCRv97/runtime/glnxa64:/opt/freesurfer-7.3.1/MCRv97/bin/glnxa64:/opt/freesurfer-7.3.1/MCRv97/sys/os/glnxa64:/opt/freesurfer-7.3.1/MCRv97/extern/bin/glnxa64:/opt/freesurfer-7.3.1/MCRv97/bin/glnxa64/libmwlaunchermain.so:/.singularity.d/libs
recon-all -s BL-101 -localGI
fs-check-version --s BL-101 --o /tmp/tmp.rbqOyn
Wed Dec  6 18:51:08 UTC 2023
 
setenv SUBJECTS_DIR /home/xna/fmri/data_BF_str
cd /home/xna/fmri/data_BF_str
/opt/freesurfer-7.3.1/bin/fs-check-version --s BL-101 --o /tmp/tmp.rbqOyn
-rwxrwxr-x 1 root root 18565 Dec  6 17:50 
/opt/freesurfer-7.3.1/bin/fs-check-version
 
freesurfer-linux-centos7_x86_64-7.3.1-20220723-115e466
$Id$
Linux xbt088 3.10.0-693.el7.x86_64 #1 SMP Tue Aug 22 21:09:27 UTC 2017 x86_64 
x86_64 x86_64 GNU/Linux
pid 106796
Current FS Version freesurfer-linux-centos7_x86_64-7.3.1-20220723-115e466
bstampfile exists /home/xna/fmri/data_BF_s

Re: [Freesurfer] Help

2023-11-24 Thread fsbuild

External Email - Use Caution

 It
 reads like something is not right with your setup/shell environment.  
 Once you have setup the freesurfer environment via, e.g., 
$ export FREESURFER_HOME=/usr/local/freesurfer/7.4.1$ source 
$FREESURFER_HOME/SetupFreesurfer.sh 
freesurfer-linux-centos7_x86_64-7.4.1-20230613-7eb8460 
Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME   /usr/local/freesurfer/7.4.1
FSFAST_HOME       /usr/local/freesurfer/7..4.1/fsfast
FSF_OUTPUT_FORMAT nii.gz
SUBJECTS_DIR      /usr/local/freesurfer/7.4.1/subjects
MNI_DIR         
  /usr/local/freesurfer/7.4.1/mni
FSL_DIR         
  /usr/pubsw/packages/fsl/current

- then the head or start of your PATH has on purpose been modified to contain 
paths pointing to binaries in the freesurfer tree,
$ echo $PATH | tr -s ':' '\n'/usr/local/freesurfer/7.4..1/bin
/usr/local/freesurfer/7.4.1/fsfast/bin
/usr/local/freesurfer/7..4.1/tktools
/usr/local/freesurfer/7.4.1/mni/bin…. rest of output deleted …
All
 python scripts in the freesurfer distribution are automatically run 
with fspython - which in turn runs the python distribution included in 
freesurfer.  Any, e.g., system, python3 otherwise found in your path 
should not be used.  We do not recommend activating a conda environment,
 or other python (virtual) environment that will change PATH or set 
PYTHONPATH after setting up the freesurfer environment.
$ which fspython/usr/local/freesurfer/7.4.1/bin/fspython$ which python3
/usr/bin/python3        <--- not used by freesurfer$ 
echo $PYTHONPATH… no output ...

- R.
Subject:[Freesurfer] HelpDate: Wed, 22 Nov 2023 08:44:18 
-0500From: Xincen Wu Reply-To:Freesurfer 
support 
list To: Freesurfer@nmr.mgh.harvard.eduExternal
 Email - Use CautionHi,I
 am using freesurfer. I have gone through with the installation and 
diagnostics and everything works fine. FOr example, using the command 
recon-all --help in terminal yields a bunch of directions. Yet, when I 
enter something like: recon-all -s bert -autorecon1an
 error pops up saying my python3 is problematic. However, I regularly 
use python3 and redownloaded it after. Please advise on the issue at 
hand.Thanks,Lucas

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail.

Re: [Freesurfer] Longitudinal LME matlab error - Matrix singular or badly scaled

2023-11-24 Thread fsbuild

External Email - Use Caution

 

Hello Sophie,

  

Just FYI, there is no matlab distribution included in the 7.4.1 release 
and we so not support using R2023b.  So I presume someone at your site 
installed R2023b separately via a Mathworks matlab installer.  We do 
provide a script, fs_install_mcr, to install either the R2014b or R2019b matlab 
runtime environment 
into the freesurfer tree for use.  I don't know if running R2019b would 
affect what you report below, but you could try it via the commands below..

  

- R.



$ export 
FREESURFER_HOME=/usr/local/freesurfer/7.4.1 
 <--- linux install path

$ source $FREESURFER_HOME/SetUpFreeSurfer.sh

<... output showing SUBJECTS_DIR and other environment variables>

$ cd  $FREESURFER_HOME/bin

$ sudo FREESURFER_HOME=$FREESURFER_HOME  ./fs_install_mcr  R2019b

I
 believe this sets things up so the libmwm* libraries are installed 
under $FREESURFER_HOME/MCRv97/bin/glnxa64.  You can try adding that path
 (or any path the script output recommends) to the start of 
LD_LIBRARY_PATH.  You should remove any other entries to a different 
MATLAB distribution.


  



On 11/23/23 20:42, Sophie Matis (sophie.ma...@sydney.edu.au) wrote:







  External Email - Use 
Caution

  
Hello FreeSurfer experts!
 
I have carried out some analysis of changes in 
cortical thickness over time using the LME Matlab (R23b) Toolbox 
distributed within Freesurfer (7.4.1) in line with the instructions on 
this page:  MailScanner has detected a possible fraud attempt from 
"secure-web.cisco.com" claiming to be 
https://secure-web.cisco.com/16TbMFKCSxY9QLMDkUoKiHpONPO8cJ5IumheTtc9oNl4e80txUMsYAc8b6sh-dB8ND2T4yKyevZcj6SoIdgd8nquWquSUgjhFRIy8HQb-wYTzCFA28w5OfBt23DxyHPwDJY7R47cWnpFBmVBjkXV7BioXniFwM9DD9P2q6dgLixlc2X1Bwx_pnJ1r2mSpL3B-A8qBrjDdcL0TzDCYzadMLqUs5uWdR2YlAZ5lA42tny6EQ_Y7PKMkw5-fjrpwzVl7CVw0oiX_WDt-wQSwceqWA3aUHgMrgjrf0P3xUxpt5_oIFpJyly4R7r3gnitkJPGNMCHgGwPhTB0UVdO1w0kNgw/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FLinearMixedEffectsModels
 
At this stage I just want to look at changes over 
time within each of three groups. For two groups I have been able to 
proceed through the steps fine and have my significance files which look
 normal. For the last group I am running into
 an error on the “[lhTh0,lhRe] = lme_mass_fit_EMinit(X,[1 
2],Y,ni,lhcortex,3); “ step. MATLAB returns “Warning: Matrix is 
singular, close to singular or badly scaled” and lhTh0 and lhRe are 
created as matrices with only NaN values.

 
Has anyone run into this error before or have any tips for troubleshooting it?

 
I haven’t had any errors on the longitudinal 
processing steps and visual QC on my files looks normal. No errors on 
mris_preproc or mri_surf2surf.  An aparcstats2table for thickness 
doesn’t reveal any NaNs.

 
My design matrix is created with X = [ones(length(M),1) M] after following the 
suggested sortData code from the wiki
Contrast is [0 1]
This is my qdec file:
 
fsid    fsid-base   yearsfromBL
108_MR1   108   0.00
199_MR1   199   0.00
199_MR2   199   1.10
199_MR3   199   2.25
202_MR1   202   0.00
204_MR1   204   0.00
204_MR2   204   1.16
204_MR3   204   2.30
223_MR1   223   0.00
0821_MR1  0821  0.00
0931_MR1  0931  0.00
1010_MR1  1010  0.00
1010_MR2  1010  1.84
1031_MR1  1031  0.00
1031_MR2  1031  1.00
1031_MR3  1031  2.13
1064_MR1  1064  0.00
1064_MR2  1064  2.01
1125_MR1  1125  0.00
1134_MR1  1134  0.00
1134_MR2  1134  1.17
1134_MR3  1134  2.28
1233_MR1  1233  0.00
1233_MR2  1233  1.05
1373_MR1  1373  0.00
1439_MR1  1439  0.00
1439_MR2  1439  1.14
1439_MR3  1439  2.28
1475_MR1  1475  0.00
1475_MR2  1475  1.04
1475_MR3  1475  2.03
1522_MR1  1522  0.00
1522_MR2  1522  2.07
1541_MR1  1541  0.00
1541_MR2  1541  1.47
1551_MR1  1551  0.00
1551_MR2  1551  0.98
1551_MR3  1551  2.05
1572_MR1  1572  0.00
1572_MR2  1572  1.03
1625_MR1  1625  0.00
1625_MR2  1625  1.06
1637_MR1  1637  0.00
1641_MR1  1641  0.00
1656_MR1  1656  0.00
1656_MR2  1656  0.94
1656_MR3  1656  2.26
1755_MR1  1755  0.00
1755_MR2  1755  1.04
1755_MR3  1755  2.01
1829_MR1  1829  0.00
09154_MR1 09154 0.00
09154_MR2 09154 1.01
09154_MR3 09154 2.01
12110_MR1 12110 0.00
12110_MR2 12110 1.04
 
 
Any help appreciated!
 
Thank you,
 
Sophie Matis |
 Data Management & Research Officer
School of Health Sciences & Brain and Mind Centre 
Faculty of Medicine and Health 

 

The University of Sydney  

Brain and Mind Centre, 94-100 Mallett Street, Camperdown (M02G) |
 The University of Sydney | NSW | 06 

sophie.ma...@sydney.edu.au 
 | sydney.edu.au
 
CRICOS 00026A
This email plus any attachments to it are confidential. Any unauthorised
 use is strictly prohibited. If you receive this email in error, please delete 
it and any attachments.
 
Please think of our env

Re: [Freesurfer] license issue with the updated version

2023-11-18 Thread fsbuild

External Email - Use Caution

 Please let us know if you are running MacOS 14 (Sonoma) on an Intel 
or silicon Mac (M1, M2 chip).    The system requirements at 
https://secure-web.cisco.com/10qwlQRot-nOOCuaXBtxsk1Ua4Tfh-PQlj0cP9-E6KzZM5idg3c7iTvMmQOzSG9PAcBrbFYMe35KnBiCn3y7IG-rVgEj0kSLvVbOHwxylEX_7qd2UpvZd0RI-joHMIjoQqJdBRMrn0pnSFHnz-SFFpzBuN9LN_tXR69BAZD8GdgOe42Qemok-1oStCPJooJ1xLsKbXOVgiFxHk0d55wZOgkW-uv9xSSB5VxhPx4QaNdwbS0mGZXww_bzMfboFOLEITeum3djwVx3EMwWM__x1IexmzFZEqSnGdgzzfIzKOYETgIxs35-X4U51g2Caz2Zn--cVCQFL8QZpew0IVrOvKA/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2Frel7downloads
 list MacOS 13 (Ventura) as the latest supported MacOS for the 7.4.1 release.
- R.

On Nov 18, 2023, at 18:29, Atena Akbari  
wrote:QObject::killTimer: Timers cannot be stopped from another thread

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail.

Re: [Freesurfer] Unable to run recon-all

2023-11-17 Thread fsbuild

External Email - Use Caution

 The install location of freesurfer under /usr/local is on purpose read 
only (like the location of most Linux package installs) so you should not be 
trying to process and write subject data there.  We provide example 
subjects under /usr/local/freesurfer/7.4.0/subjects for read only purposes.
Neither can you set SUBJECTS_DIR or write files in the process of running 
recon-all to your mounted or shared C drive.  This is because the the 
Windows file system does not support creating soft links.
So please try the following.  In your Ubuntu linux terminal window, 
 go to your HOME directory and create a subjects directory there, i.e., 
you can always read/write to your HOME directory.   Then copy in your 
subject data to be processed there via recon-all and set SUBJECTS_DIR 
appropriately or pass the path on the recon-all command line.
… in WSL linux terminal window …$ cd $HOME$ mkdir subjects$ cd subjects$ 
pwd/home/naily/subjects$ export SUBJECTS_DIR=/home/naily/subjects… copy in your 
data to process for recon-all to live under SUBJECTS_DIR …
It also looks like your license file is not being found.  You can set the 
environment variable FS_LICENSE to point to that so it will be found and read,
$ export FS_LICENSE=/home/naiy/license.txt$ head -1 
$fs_license...@somewhere.com       < email address 
you used to register
… then try running some Freesurfer commands again …
- R.
On Nov 17, 2023, at 17:49, Nai, Ying Hwey  
wrote:

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail.

Re: [Freesurfer] Question about Freesurfer

2023-11-06 Thread fsbuild

External Email - Use Caution

 Hello Mahdi,
If you have not already done so, you might want to look at the Freesurfer wiki 
notes about setting up an X-server on Windows so linux applications running in 
WSL can display graphics using 
X-windows, https://secure-web.cisco.com/1IeFJcAKROeUNyLVra8oNytGyzB-WvQhRkz3GN5_1Txy8oLFJDQUo-f8ZHzfjyZbyVGPM2mROYYBy22fnlN-kl_e23yBKEtB2DuEOJAe7sMTh64Q9HrFUmTU9XkuGeXTsrOc8KHmXQAru1qVCQpeLRlHb_UlVrEln22ennkW4QVIlF3A1Z0_9LOFKxQc6gPA5a7Hes1Yiks3GPrZM2SAnxS746Sqe4v42HiUmSvhXBYz5x_rY2DsC-geI6mWT9kQPjE7fLUoEWBzflVj9ELIaJv7w_mi0ozeErVsyB9F1FKKK74RMrvBaLWfE18vMaWao/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFS7_wsl
  The setup listed there is for Xming, and you may want to look at both 
https://secure-web.cisco.com/1yLpWBJBzFQsVnx0Ncp8u61K6nbDOQ5sj4Uh-OSMos9GTrEDmiKo-ITzLOwI8tAWHPIzbOfOAECxeDE0ldl04hOCd1VkriFGjCqauUCZLbdmqbqUCV7ZayjK_Mc2TdhwhkmNs0k0YvCS4OScvNeTPTTOeOjiAaXXNPtFyCxd5w6wS2AsCdMKjy_J3qpeGWDsjRBRo8Fbqk20r3GbcGF3dkytO-RfOQddZnYExK2eFjL7gQztEIxlKKLJpJP6AIKPL6iR-9hw2xmWVNqYA4_wpBNR4s9k4kWhTYlK6VV4ggvzHmZlkjVDQqFNZLQX1eFsq/https%3A%2F%2Fsurfer.nmr.mgh..harvard.edu%2Ffswiki%2FFSL_wsl_xming
 
and https://secure-web.cisco.com/1STa8uko59yOcskM83ifwl-XKlLZOFpLQkufkYvxaMiNrWGCUMSwNctfrOfWtxpDsMvgHMnnx2h962-7-iLdFPsHVZDwgftFM52ZJqTOD5UeR4F8NFlt42lsbArYyaGmYV8WviUXXcc7xfeDfoNDNpfQYifN1mwrnRpMMcSkNJQCP9BLO23bex9_5A-rTHQ8uuiqNz9a2c5NRcGCMAWA4MZY8iTyQ4IlNhWb7BV_QQw-x_1DZULmDt9Pg2N6mICwfVoNe88iP9-TDc-Uu5KlgvfrnAUmv_XPdWdmocW0fz3kt6F-6eZd7jzvrJ9gdM7m6/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFS7_wsl_ubuntu
Some people have found Moba 
X-term, https://secure-web.cisco.com/1ZVDzOuRds29V2esWHXhtFh_3s3wsJpkWd0i5e_OhneoPEY-dRlrXFon9sw9CxIOt6JtTwbqDcDKyeZYcfzbcHgvrp0yvwPFO-RNdG8UaZ8Q74wFaRwDMXrjYr9LFAkLp4Xak6tyOjbwZZUG5nIKgJmrNXimNrEnLbPpJDVkb1_Kg2I_bKnJgP50HXwHd52t2CSISPv94DQVYc36hP4AOD6ZyITwrGDmW9E6uW-b-2cXENpciP_ca60m9tMYC5-8F9aJV7BXDyFuh45TY1O56nqRfWJFI3p7IYBY98jcZdMPgCzTZihcLHNoIYj-VvDo4/https%3A%2F%2Fmobaxterm.mobatek.net,
 easier to setup and test with glxgears compared to using Xming.
It’s a good idea to get glxgears to display the spinning gears in an X-Window 
before trying to run freeview.  Or the display of glxgears can work, but 
freeview may still display a black/empty screen.  That can be from the 
graphics card drivers on the Windows host not being up to date or not 
supporting more recent versions of OpenGL.
There are also quite a few postings about WSL on the freesurfer list.
- R.

On Nov 6, 2023, at 13:48, Mahdi Babaei  
wrote:External Email - Use 
CautionThanks for the 
reply.Yes, glxgears command shows a blank window. I thought about it but 
couldn't find any solution. I'm working on WSL2.Best,MahdiOn Mon, 6 Nov 
2023 at 13:16, Wang, Ruopeng  wrote:It sounds 
like an openGL rendering issue. If you run glxgears command, do you see a blank 
window or spinning 3D gears?RuopengOn Nov 6, 2023, at 12:37 PM, Mahdi Babaei 
 
wrote:External Email - Use 
CautionHi Paul,Thank you for 
your response. There was an issue with my description. I meant to refer to 
volume data. Freeview is displaying a black view, even though it loads the 
images. Unfortunately, nothing is visible.Best,MahdiOn Mon, 6 Nov 2023 at 
11:30, Wighton, Paul  wrote:Hi Mahdi,I'm afraid 
I don't know what you mean by "Freeview opens fine but when I load a column in 
it just shows a black view."  What is a column in this context?As for 
registration between PET and MR, have you seen this page?MailScanner has 
detected a possible fraud attempt from "secure-web.cisco.com" claiming to 
be https://secure-web.cisco.com/1b4i3XSSINjUpxeaKg1CHfqqMtsa2ceG8AjVCHbWEJFS_lJ1b-QMOCffk_k0_xcQLsD-qCcYCkoyHek35mgBwuIOGexxlOuDvLm5xVvYNo2JiaWRbGhas9yUvDTZzuZ4x8eo_HNtPss2f1KBg1Bj_m_vrSBDH2Emrjz_c3Q8JhFAsYV3fiwnUEUCM1k7o6deyZs8tmtC36Vv5MK7Jj9HRzZ6TyfJWxDy2zALLdkYSqKyAIbDRC-C-XrKIWL644j_VMEQHeqUPwwsGlc08i28HJL6MZ3zqjQ7SAcChI8K1XNPhKGHAsRN1vYTlLrnsB6qE/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FPetSurferIt
 suggests using 
mri_coreg.-PaulFrom: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Mahdi Babaei Sent: Sunday, 
November 5, 2023 2:25 PMTo: freesur...@nmr.mgh.harvard.eduSubject: 
[Freesurfer] Question about Freesurfer        External 
Email - Use CautionDear FreeSurfer Team,I'm currently a PhD student at Stevens 
Institute of Technology in New Jersey, USA, where my research focuses on MRI to 
PET translation. I have a number of problems. Freeview opens fine but when I 
load a column in it just shows a black view. Have you ever encountered this 
problem?I'm so confused about using the tool for registration. Can I do 
registration between MRI and PET modalities of the same subject using 
"bbregister"?Best,Mahdi__

Re: [Freesurfer] Freesurfer crash when loading "volume" surf

2023-10-26 Thread fsbuild

External Email - Use Caution

If you have been launching Freeview using the Finder by double clicking on the
icon, then try running it from the command line in a terminal to open a file,
e.g. in bash or zsh ...
$ export FREESURFER_HOME=/Applications/freesurfer/7.4.1$ source
$FREESURFER_HOME/SetUpFreeSurfer.sh… output deleted ...
… set the environment variable FS_LICENSE to point to your license file, e.g.,
put license.txt file you received via email after you registered into your home
directory under /Users/ ...
$ export FS_LICENSE=$HOME/license.txt$ head -1 $fs_license...@somedomain.com.
<— email address you used to register with
$ which freeview/Applications/7.4.1/bin/freeview
… test displaying a known to be good volume …
$ freeview $SUBJECTS_DIR/bert/mri/brain.mgz
If the above works, then try opening your file(s) from the command line instead
of the volume file listed above.
- R.

On Oct 26, 2023, at 20:42, Mirsol Choi
wrote:External Email - Use
CautionHi there, I have
processed a t1 image using recon-all function, and when I try to open the
surface file "lh.volume" or "rh.volume", freesurfer crashes everytime. This
crash also occurs for other surface files as well, such as
"lh.area.pial". Attached is the error message, do you know how I can go
about this?For your reference I am using a macOS, running freesurfer
7.4.1.Thank you, I look forward to hearing from you. ___Freesurfer mailing
listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] Freeview issue

2023-10-22 Thread fsbuild

External Email - Use Caution

 

The Qt graphics libraries may need virtualGl over a 
remote X connection.  So try prefacing your freeview command with 
"vglrun".  See the introductory text about vglrun and the install commands 
on this page, 
https://secure-web.cisco.com/1_jeLuB9K3YFX-_vkUZquNAqePEbWUSsW-inupVmdbjXlex4rhufV8pNS0NPj6_HwmfTXNTHj-f1VpwO5L1FxVZxjTuZd_jIKlPJYkhBZ0iXvHGrpj7gUiuE2Lt9vAZeu4ieazTNok61_W9Fp6jv7ukbRi4jmQb63yTPmjlf8IpULZuGieE0qGkioK4gcDBDplqwVm2PqqQMutUxdvd0z6GI-TTBv2AO2A7sAqo_dHWkHoPVMDaUl6alNIUg8L8JeYe3Rn_pHVqDrgHUhSpcXzqgCp6DA-cdBz0bQoVnRi_CXCU8BaXBwqbrOUYck_W1vMDl_8y3cgoynupChWihsJAmC-LOIkKi9YdqpiuqCh5U/https%3A%2F%2Fwww.starnet.com%2Fhelp%2Fvirtualgl%2F
Then once the remote display of images is working, you might run into an issue 
trying to map the display size to your
 remote screen resolution.

  

- R.



On 10/22/23 03:57, yunus soleymani (soleymani.yu...@yahoo.com) wrote:



  External Email - Use 
Caution
  I did the following codes 
respectively:> cd> wget MailScanner has detected a 
possible fraud attempt from "secure-web.cisco.com" claiming to be 
https://secure-web.cisco.com/11GVLnIDWxo_vR8D2Oa9AP0rLkOmLrhl51L-g0K4pY8mWNpc25hCXYg5qw8EPIDzfeeqnv5cyYNzMcPC4QuvC50tzwwJorW1AfzALLGmEBRBXCgyXxcZc_hE7PwJ4tlnTT6sGRSjGObyGuLSiWR2CqZwl8RzH1BkEi9Ym8xXnYWGsmvBrglSgH16t-SgIKgF6aa5ME4NabctEizZwF8Z-I-2GkQcbaTmEQswaBOEXeplL7RIF-NDXzFrqplw2TJ5IOZ20pTaB80VCXGMqxLxT39ijfH-d0u5-loTVFRtTYIfeFpKjtCAO_Q304dRytXSKFjZ5De30yK8NnZkJ9fATbgdcDc9KYYSfx1p0yFs8GJQ/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Fpub%2Fdist%2Ffreesurfer%2F7.4.1%2Ffreesurfer_ubuntu22-7.4.1_amd64.deb
> ls freesurfer_ubuntu22-7.4.1_amd64.deb
> sudo apt-get update -y
> sudo apt-get -y install ./freesurfer_ubuntu22-7.4.1_amd64.deb
> export FREESURFER_HOME=/usr/local/freesurfer/7.4.1
> echo "export FREESURFER_HOME=/usr/local/freesurfer/7.4.1" >> 
$HOME/.bashrc
> ls $FREESURFER_HOME
> ls license.txt
> echo "export FS_LICENSE=$HOME/license.txt" >> $HOME/.bashrc
> echo "export XDG_RUNTIME_DIR=$HOME/.xdg" >> $HOME/.bashrc
> echo "export DISPLAY=:0" >> $HOME/.bashrc
> echo "source $FREESURFER_HOME/SetUpFreeSurfer.sh" >> 
$HOME/.bashrc
 .
 The
 above codes all worked correctly and the software was installed 
successfully. Also, the software analyzes the subjects correctly by 
using parallel recon-all code. The only issue is that the Freeview 
interface doesn't work and the error mentioned above appears. Is it 
because of that I am using a remote desktop connection tool to connect 
to my institute servers?


Yunus
 Soleymani
Ph.D. Candidate of Neuroimaging Tehran University of Medical Sciences
MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" 
claiming to be MailScanner has detected a possible fraud attempt from 
"secure-web.cisco.com" claiming to be soleymani.yu...@yahoo.com+98 914 526 
9298--------






  



On Sunday, October 22, 2023 at 11:12:08 AM GMT+3:30, 
fsbuild <fsbu...@contbay.com> wrote:





External Email 
- Use Caution Wondering
 if you used the freesurfer_ubuntu22-7.4.1_amd64.deb installer package 
from the download page and installed it from your Downloads folder via,$ sudo 
apt install ./freesurfer_ubuntu22-7.4.1_amd64.debThe link for that file on the 
downloads page MailScanner has detected a possible fraud attempt from 
"secure-web.cisco.com" claiming to be 
https://secure-web.cisco.com/1P6sJsKdfjhSOlm7uHbTXJ8nsEFCHNYGKzdj0djukhVoPCyG91EdBhVxbHi53kwpdQYCT-ByuHLRTukUzTBvHVUXJo03E4wEptjCsZFOVgHNqY15mUXlHsG7f_vvg0sAtr1BNs0Zq8iy1MDkYvqy_XHV1uXFLEzVBxejhxdjQTN5CXaz8hynqEdriY2-0tNSKP0TeFutwa5N8m6gYsk9nXS75QwEy1K3knJhXby-Pm_ZYQ_1LXXTArPv-7n0rrxguvS0zsbj-5MiODIlxB2KbSgy267kxc-qAcb_bj1_9j9MlCZjv_0PHnxJn8SSicHG5S2qZxz31VQe-xgh-gooxtMr4pSp0hF9d3j2pX8pAUVI/https%3A%2F%2Fsurfer.nmr.mgh.harvard..edu%2Ffswiki%2Frel7downloads%26nbsp;is https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/7.4.1/freesurfer_ubuntu22-7.4.1_amd64.deb-
 R.On Oct 22, 2023, at 02:19, yunus soleymani <soleymani.yu...@yahoo.com> 
wrote:External Email - Use 
CautionI have the same 
problem. I would greatly appreciate your help with 
this.Yunus
 SoleymaniPh.D. Candidate of Neuroimaging Tehran University of Medical 
SciencesMailScanner has detected a possible fr

Re: [Freesurfer] Freeview issue

2023-10-22 Thread fsbuild

External Email - Use Caution

 Wondering if you used the freesurfer_ubuntu22-7.4.1_amd64.deb installer 
package from the download page and installed it from your Downloads folder via,
$ sudo apt install ./freesurfer_ubuntu22-7.4.1_amd64.deb
The link for that file on the downloads 
page https://secure-web.cisco.com/1_35_maf1qeyDwN-YbnCQ8jOb6jvY5lINnAzztz0hRLD0JseUsdcHLQQn-9oN4Xf-0aaTL-xA7oSZSleQrdE_yI-urkuo_8dbOO2aiY13AYtsJTRILkzHGZi1TGwCD8Ywi8woTfAO3wh_9v1Xgux9lnFhVCVb_XtZeAmupzyWe44oapIbnV7FxQ-SHiFFd6No6MeMtAV2bj4l_Tb0oyF4xPb51zNX2UW4sCtlr3XDT3E_jZWpa7Wfg9OutA3mWKZX-EwQZS83QmQEdq_lPlHr69Ck5qqSVMhCUnNw8b5MrCyOZpcPbS4WKnC6_OQaSXxyUhRdO_phUm9N6pB0UhdiYAatDutIdTKQI-qx-8lpM-g/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2Frel7downloads%26nbsp;is https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/7.4.1/freesurfer_ubuntu22-7.4.1_amd64.deb
- R.

On Oct 22, 2023, at 02:19, yunus soleymani  
wrote:External Email - Use 
CautionI have the same 
problem. I would greatly appreciate your help with 
this.Yunus
 SoleymaniPh.D. Candidate of Neuroimaging Tehran University of Medical 
SciencesMailScanner has detected a possible fraud attempt from 
"secure-web.cisco.com" claiming to be MailScanner has detected a possible fraud 
attempt from "secure-web.cisco.com" claiming to be soleymani.yu...@yahoo.com+98 
914 526 
9298On
 Saturday, October 21, 2023 at 12:24:10 PM GMT+3:30, Ramesh Babu 
 
wrote:External Email - Use 
CautionDear Expert,Recently I 
installed the latest version of freesurfer in Ubuntu OS 22LTS.. Freesurfer is 
installed successfully, but freeview gives some errors which I pasted below. 
Please provide your suggestions. Thank YouRameshfreeview This 
application failed to start because no Qt platform plugin could be initialized. 
Reinstalling the application may fix this problem.Available platform plugins 
are: eglfs, linuxfb, minimal, minimalegl, offscreen, vnc, wayland-egl, wayland, 
webgl, xcb.Aborted (core 
dumped)___Freesurfer mailing 
listfreesur...@nmr.mgh.harvard.eduMailScanner has detected a possible fraud 
attempt from "secure-web.cisco.com" claiming to 
be https://secure-web.cisco.com/1BZ4_HvToI5a6OuM5gIFWs2VyFinjkWLi8C5L5ny7WeSkoUPm5JKinKYGrfFLsEEF6vXjSSB20skB1EH-5lApynTVgrUWDRK6SYlzq7r_QITnqNOo7cdyNRDmeFg2IBypvUo11FF3iBvcCmldzGq4fUTBIXuuSU6A6hFQcj0jB-aOU055LyuED92RNGc3XyiZ5YqQI0p57CfVu0qZZlh-KwwTsUcpaxB0tdN7hR3-W5uhj2D2OK1GW5QBa4Dg9hc3fxMFboPH8PBvkJstq_3knPEMjnYxzfa0osNnEkqDYsyi_mQ01W0AvSIB65LMi-IKrNLcMNXAUF1tW-I5QZLaPvx6PAtiBikmWKoFykv5bRg/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer___Freesurfer
 mailing 
listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail.

Re: [Freesurfer] fsxvfb error: Falling back to using screens root_visual

2023-10-20 Thread fsbuild

External Email - Use Caution

I could be wrong, but it reads like those errors are from the libqt5xcb.so 
running into errors
 communicating with X windows.   Since freeview runs fine displaying 
those images on the machine when not exec'd thru fsxvfb, then maybe fsxvfb 
cannot 
capture because it is not expecting freeview to (still) run using Qt
 graphics and X-windows .  I believe the release notes say fsxvfb 
does not need an X-server and so perhaps it is trying to capture images 
directly from the graphics hardware.  Could be something is not up to 
date on your system with the graphics hardware drivers/system libraries.



Another thing to consider is the freesurfer 7.4.1 release was not built 
for nor tested on Ubuntu 16 - the minimum version tested was Ubuntu 
18.   Given you are running it from the path 
/usr/global/freesurfer/7.4.1 then I suspect you did not download and run
 the 7.4.1 debian package installer for Ubuntu 18 as recommended on the 
freesurfer download page,  
https://secure-web.cisco.com/1pa_Juw1rvYdwKxiYGrhHioNA_vUa-3QRuSL2A9WRhRTgvRuNTlbqumOYdkFLoeMjU_rWgh1UP8tarqEvB5UE6aoIgGhJvYzzrbdKfm3dpEYTLfVNPmASjXkZ5aqziSPs85bAm9uH5jJwateGLOqKDRl5GoCIe7ehl-qH_X8_8P63d8JsR4oALTRtN1Wo_Q8vkZRIap_xWTZZbWuNQPxDafEOVwKLfvbUUBstFI3f5vpPbNFdrpaxaiy8nTlmnsZN8RL33Ley7Izxbed5ctd5K7Re0lBjXiMqHamlrTOd_MKaUcBQjowAxDqNgre2l05H/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2Frel7download
 (which would 
install under /usr/local/freesurfer).   It would not be surprising for 
the Ubuntu 18 binary installer to fail trying to update an Ubuntu 16 system, 
but you could try running it.  You can 
decline/abort the installation if you don't approve of the system 
updates it reports are needed before installing freesurfer.  Even if
 the installer succeeds, we can't guarantee 7.4.1 will work correctly on
 Ubuntu 16.



- R.
On 10/19/23 17:50, Dani Del Rubin (rubin...@ohsu.edu) wrote:


QXcbConnection: XCB error: 1 (BadRequest), sequence: 167, resource id: 133, 
major code:

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail.

Re: [Freesurfer] Freeview misaligned surfaces "warning matrixinverse failed"

2023-10-17 Thread fsbuild

External Email - Use Caution

From what I can see, the freesurfer release 7 installers do not modify the 
shell init file, e.g., bashrc, and neither did the VM provided in the past with 
freesurfer 7.2.0 pre-installed have an entry with FS_DISABLE_LANG set in the 
bashrc file.
- R.

On Oct 17, 2023, at 06:04, Marina Fernández 
 
wrote:External Email - Use 
CautionHi Andrei and Freesurfer 
experts,We had the same problem in the past and we noticed there was an extra 
line in the .bashrc file of Ubuntu: export FS_DISABLE_LANG="true"Deleting 
this line solves the problem. The .bashrc file should contain only the 
following FS lines:#Freesurfer:export 
FREESURFER_HOME=/usr/local/freesurfersource 
$FREESURFER_HOME/SetUpFreeSurfer.shMake sure you do this for home and root 
.bashrc files.Hope this helps.Best 
wishes,Marina___Freesurfer mailing 
listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail.

Re: [Freesurfer] ERROR: could not configure recon-all parameters

2023-10-15 Thread fsbuild

External Email - Use Caution

 

Just FYI, it is not intended that you process your 
own subjects using SUBJECTS_DIR set to a path under where freesurfer is 
installed, i.e., SUBJECTS_DIR in the log is set to,

  

  setenv SUBJECTS_DIR /Applications/freesurfer/subjects/recon-all

cd /Applications/freesurfer/subjects/recon-all/MR7312_501/surf

  
  

Writing files there normally fail without the sudo command, 

% touch /Applications/freesurfer/foo

touch: /Applications/freesurfer/foo: Permission denied
That will prevent recon-all from being able to create soft links.  Neither 
should recon-all be run with the sudo command or that 
path 
down-protected to allow writing files there w/o the sudo 
command.




After the setup of the freesurfer environment with,




  
$ export FREESURFER_HOME=/Applications/freesurfer/7.4.1
  

  
$ source $FREESURFER_HOME/SetUpFreeSurfer.sh
  

  
 freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 
  

  
Setting up environment for FreeSurfer/FS-FAST (and FSL)

FREESURFER_HOME   /Applications/freesurfer/7.4.1

FSFAST_HOME       /Applications/freesurfer/7.4.1/fsfast

FSF_OUTPUT_FORMAT nii.gz

SUBJECTS_DIR      /Applications/freesurfer/7.4.1/subjects

MNI_DIR         
  /Applications/freesurfer/7.4.1/mni
  



- then change SUBJECTS_DIR to point to a directory where you already 
have write permission like somewhere under your home directory,



$ cd $HOME

$ pwd

/Users/<your userid>

$ mkdir -p $HOME/subjects



 and reset SUBJECTS_DIR to point to the path you just made ...



$ export SUBJECTS_DIR=$HOME/subjects

$ echo $SUBJECTS_DIR

/Users/<your userid>/subjects



Then try running your commands.



- R.



On 10/15/23 20:19, 윤혜정 (hyejung7...@amc.seoul.kr) wrote:



  External Email - Use 
Caution
  Hi Yujing, 
Thank you for your help. I see it works now. I have attached my recon-all 
log for you to see. Can you please go through it and confirm that it has 
no errors? 
Thank you. 
Best,Alice -Original Message-
From: "Huang, Yujing"<yhuan...@mgh.harvard.edu> 
To: "Freesurfer support list"<freesurfer@nmr.mgh.harvard.edu>; 
Cc: 
Sent: 2023. 10. 13. (금) 20:54 (GMT+09:00)
Subject: Re: [Freesurfer] ERROR: could not configure recon-all parameters
 







lh.pial and rh.pial are created as symbol links to lh.pial.T1 and rh.pial.T1.
rh.pial -> rh.pial.T1
lh.pial -> lh.pial.T1
 
Do you have lh.pial.T1 and rh.pial.T1 in your surf/ directory? 
 Symbol links may be disallowed for your machine. Can you attach 
recon-all.log?
 
Best,
 
Yujing
 


From: freesurfer-boun...@nmr.mgh.harvard.edu 
<freesurfer-boun...@nmr.mgh..harvard.edu>
On Behalf Of ???

Sent: Thursday, October 12, 2023 9:32 PM

To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>

Subject: Re: [Freesurfer] ERROR: could not configure recon-all parameters


 
External Email - Use 
Caution


Thank you for your swift reply. I will try that soon.


 


I
 have other pack of data that finished recon-all process and I don't 
have lh-pial & rh-pial to view on freeview for some reason.


I have the same problem for all of recon'd files. 


Is this another recon-all error or is this just my data problem? 


 


Thank you in advance.


 


Best,


Alice

 
-Original Message-

From: "fsbuild"<fsbu...@contbay.com> 

To: <freesurfer@nmr.mgh.harvard.edu>; 

Cc: <hyejung7...@amc.seoul.kr>; 

Sent: 2023. 10. 13. (금) 10:04 (GMT+09:00)

Subject: Re: [Freesurfer] ERROR: could not configure recon-all parameters

 
External Email - Use 
Caution
 

It looks like permissions on the installed freesurfer files and/or what you set 
FREESURFER_HOME to may not be correct.

 


I 
would delete your current freesurfer install and then use the Mac 
installer package (.pkg) file to install the 7.4.1 release.  That should
 ensure all the file privileges
 are correct so the files can be executed.  You will need sudo 
privileges for these commands.


 


… open a terminal window and delete the current freesurfer installation …


 


$ cd /Applications


$ sudo  rm -rf freesurfer


… you will be asked to enter your password ...


$ cd


 


Download the 7.4.1 package installer in your browser using the 
link, MailScanner
 has detected a possible fraud attempt from "secure-web.cisco.com" claiming to 
be 
https://secure-web.cisco.com/16QsjI_IFOK8Xo0B1gMl3uWmO7oo4wVgTL1WN7x8nR916ZXpeDKxxuAWopZIjbfqH72qVw4Ms5TqQNmSvrAeAYV_mOKhiwg0yIYNx8fsLKI-nL7x3tgxF3-2bl0EIwA2SBk-At_d1hnfHcIEMYX8crxT7XRLsiknyl8FOQGRAGE4ToF4KANVZoZe6cLpfQ-CrV_EnA1KG9AIAJm9_wfyCQ7DF_YvNwdxGTGTgWPThn7eL2JLYtrb8A7rCmFbhjnPn1gA5y1_SzPvM2BfefpFMSwZrY8lMB68UFHpUvkWy-YdmWhYqq7jjo01KKnfXS1weRikAyDcnqCNx5nwpw3r5tQ/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Fpub%2Fdist%2Ffreesurfer%2F7.4.1%2Ffreesurfer-macOS-darwin_x86_64-7.4.1.pkg


 


In a 
Finder window, open your downloads fo

Re: [Freesurfer] ERROR: could not configure recon-all parameters

2023-10-12 Thread fsbuild

External Email - Use Caution

 It looks like permissions on the installed freesurfer files and/or what 
you set FREESURFER_HOME to may not be correct.
I would delete your current freesurfer install and then use the Mac installer 
package (.pkg) file to install the 7.4.1 release.  That should ensure all 
the file privileges are correct so the files can be executed.  You will 
need sudo privileges for these commands.
… open a terminal window and delete the current freesurfer installation …
$ cd /Applications$ sudo  rm -rf freesurfer… you will be asked to enter 
your password ...$ cd
Download the 7.4.1 package installer in your browser using the 
link, https://secure-web.cisco.com/1IMDK1N7QCuFHDBAqbwgRc9pMUoAwzPh8gLV8fwqcUUSZYNUAtkffWnRycsKB-8aNNnZecU30n-LThO_rOXYp_BKdmP4uubAna6GBikj7uoKKAxWfyg0ltpvrbJnznjM8ucu72-EvDBWInryq7Ln74QipZqxLutAiwYkTxTfnUkivop9wJVFh0s1PQ9CtingaAKSC8c7Yk7RwvdfDO1oluWK8W6H2YfS_gGIaXQ0DJ6BnDUBKXr0dWCSg_9I_BURx9B-tLkNE3-Ttz90_Xj_KZDRoeRCc0aktbHn95GmKLFrNW7XWArvn-2qLFEOsyJZmqOFvuxWTt9rNdoUoDXxnUQ/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Fpub%2Fdist%2Ffreesurfer%2F7.4.1%2Ffreesurfer-macOS-darwin_x86_64-7.4.1.pkg
In a Finder window, open your downloads folder (or go to wherever you 
downloaded the .pkg file).  Then RIGHT CLICK with the mouse on the icon 
for the file freesurfer-macOS-darwin_x86_64-7.4.1.pkg and select “Open 
With” installer.app (default).   Select “Open” when the installer opens a 
new window asking if you want to do the install.  Click thru the installer 
options by selecting “Continue” and accept the license, etc.
… when the install is done, setup the Fresurfer environment in a terminal 
window …
$ export FREESURFER_HOME=/Applications/freesurfer/7.4.1$ source 
$FREESURFER_HOME/SetUpFreeSurfer.sh 
freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 Setting up 
environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME   /Applications/freesurfer/7.4.1
FSFAST_HOME       /Applications/freesurfer/7.4.1/fsfast
FSF_OUTPUT_FORMAT nii.gz
SUBJECTS_DIR      /Applications/freesurfer/7.4.1/subjects
MNI_DIR         
  /Applications/freesurfer/7.4.1/mni
… check python3 is there ...
$ ls 
$FREESURFER_HOME/python/bin/python3/Applications/freesurfer/7.4.1/python/bin/python3
… then try running freesurfer commands again …
- R.

On Oct 12, 2023, at 20:01, 윤혜정  
wrote:External Email - Use 
CautionHi,  On top of 
the email I sent earlier, I also get the next error line that says: ERROR: 
could not configure recon-all parameters/Applications/freesurfer/bin/fspython: 
line 20: /Applications/freesurfer/python/bin/python3: cannot execute binary 
file /Applications/freesurfer/bin/fspython: line 20: 
/Applications/freesurfer/python/bin/python3: Undefined error: 
0 -Original 
Message-From: hyejung7...@amc.seoul.krto: ; Cc: Sent: 2023.
 10. 13. (금) 08:35 (GMT+09:00)Subject: ERROR: could not configure 
recon-all parameters Good day,  I get the following error 
message when I run recon-all: ERROR: could not configure recon-all 
parameters/Applications/freesurfer/bin/fspython: line 20: 
/Applications/freesurfer/python/bin/python3: cannot execute binary file I 
went through a bit of the mail archive and unlike the others I don't see ASCII 
error message in mine.  Additionally, I was wondering if the 
thickness of MR slices would affect recon-all process at all?  I 
appreciate your help.  Best 
wishes,Alice ___Freesurfer 
mailing 
listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail.

Re: [Freesurfer] Hippocampus Segmentation Troubleshoot - Matlab crash

2023-10-09 Thread fsbuild

External Email - Use Caution

Please try using the Matlab runtime environment which can be installed directly 
into the freesurfer tree via a script we provide.  The runtime environment 
is free and requires no paid for Matlab license (since it does not include the 
Matlab compiler).
For your existing install of freesurfer 7..1.1, the tested version of the 
Matlab runtime environment to install is R2014b (listed below as the version to 
use in the bash/zsh commands).  However, if you were to update to the 
current freesurfer 7.4.1 
release, https://secure-web.cisco.com/1EbuUGpusH65Vnhqyq32iw8lhOzpyphGTkomb1eGIHw58FD4ikSbt9f7VFH4X8deyqrzjKVzFMgqki-n63sKgin2kguxnvVJ0g1kgDFvZDwcE9MYyz4PxA482Uoppvj_xzoJ7FZfWzjxTRMYqj7SGcDj6ClpBf7YSyiSYJPwYvPDbNKVzBl_68uYwiEBaf4tA7hhc2wAcVv-dTmneINRGW4ayp1zoonJKmUYUsD5NNzRTiy0JBh5uS3MTuHXb8gq_Vb9DwI2znfq2inPePbqtqJtHEU4X372cxYJRMx9L8Q6tGQsl51lXryVbRgi7Mq5L7zTZ2UN8gInW9BnhIgczuQ/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Fpub%2Fdist%2Ffreesurfer%2F7.4.1%2Ffreesurfer-macOS-darwin_x86_64-7.4.1.pkg,
 then you could use the more recent R2019b Matlab runtime.
$ export FREESURFER_HOME=

$ cd $FREESURFER_HOME/bin

$ sudo FREESURFER_HOME=$FREESURFER_HOME  ./fs_install_mcr  R2014b 
   <— change to R2019b if you end up using freesurfer 7.4.1

… answer y to any installer questions …

The output from running that script will list what DYLD_LIBRARY_PATH 
should be set to.  

Please make sure you have otherwise removed any references to your previous 
matlab environment from DYLD_LIBRARY_PATH, PATH, etc.  It might also work 
to add $FREESURFER_HOME/MCRv97/bin/glnxa64 to DYLD_LIBRARY_PATH but I would 
first try what the script prints out as the local paths on your machine.
- R.

On Oct 9, 2023, at 20:21, Mirsol Choi  
wrote:External Email - Use 
CautionHi there,I am a Master's 
student who is looking to segment the hippocampus and analyze diffusion data of 
the segments. I am trying to utilize the segmentation function with 
this command:segmentHA_T1.sh subj01But I am met with this error saying that 
Matlab has crashed. The crash log is attached to this email. I have 
freesurfer version 7.1.1, running on MacOs 11.7.10.I have followed your website 
instructions to download Matlab R2014b.Following the installation process 
of Matlab, I was met with this message: Installing 
Product: MATLAB Compiler Runtime - Core 8.4(Oct 08, 2023 11:29:15) 
Installing Product: MATLAB Compiler Runtime - GPU 8.4(Oct 08, 2023 
11:29:21) Notes: On the target computer, append the following to your 
DYLD_LIBRARY_PATH environment 
variable:/var/folders/zz/zyxvpxvq6csfxvn_n0/T/tmp.aMmBemHB/install-target/v84/runtime/maci64:/var/folders/zz/zyxvpxvq6csfxvn_n0/T/tmp.aMmBemHB/install-target/v84/sys/os/maci64:/var/folders/zz/zyxvpxvq6csfxvn_n0/T/tmp.aMmBemHB/install-target/v84/bin/maci64:(Oct
 08, 2023 11:29:21) Exiting with status 0(Oct 08, 2023 11:29:21) End - 
Successful.FinishedR2014b installed successfully in 
/Applications/freesurfer/7.1.1/MCRv84And so I have appended the path using this 
code into my bashrc profile: export 
DYLD_LIBRARY_PATH=$DYLD_LIBRARY_PATH:/var/folders/zz/zyxvpxvq6csfxvn_n0/T/tmp.aMmBemHB/install-target/v84/runtime/maci64:/var/folders/zz/zyxvpxvq6csfxvn_n0/T/tmp.aMmBemHB/install-target/v84/sys/os/maci64:/var/folders/zz/zyxvpxvq6csfxvn_n0/T/tmp.aMmBemHB/install-target/v84/bin/maci64I
 am wondering if I can get some help with running the hippocampus segmentation 
protocol .Thank you so much for your time, I greatly appreciate your 
support. ___Freesurfer
 mailing 
listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail.

Re: [Freesurfer] $FREESURFER_HOME/bin not being added to PATH (tcsh)

2023-10-09 Thread fsbuild

External Email - Use Caution

If you add these 2 commands to setup the freesurfer environment, e.g., for 
csh/tcsh as your default shell,
$ setenv FREESURFER_HOME /usr/local/freesurfer/7.4.1-1$ source 
$FREESURFER_HOME/SetUpFreeSurfer.csh
- to your shell initialization file, $HOME/.cshrc, then FREESURFER_HOME, 
SUBJECTS_DIR, PATH, etc., should automatically set/modified by source'ing 
SetUpFreeSurfer.csh when you open a new terminal window.   There is no 
need to subsequently set SUBJECTS_DIR or other freesurfer environment variables 
in your shell init file (or in the current terminal window session) unless the 
settings should be different than the defaults.  Most people add those 2 
commands to be the last 2 lines in their shell init file.
I would check the defaults set in the current shell environment using only 
those 2 commands above in your shell init file after opening a new terminal 
window,
$ env | sort
… and check FREESURFER_HOME, SUBJECTS_DIR, PATH are set …
The freeview command should already be found in your path, i.e., you should see 
…
$ which freeview/usr/local/freesurfer/7.4.1-1/bin/freeview
- R.

On Oct 9, 2023, at 14:56, Edward Zuniga  
wrote:External Email - Use 
CautionHello,I am attempting to 
install FreeSurfer on a Centos 7 workstation using the tcsh shell. Below are 
the contents of my .cshrc file. Should $FREESURFER_HOME/bin be 
automatically added to the PATH? I tried rebooting, and it still is not 
adding it to the PATH. My environment variables appear to be set 
correctly  because I see this when opening a new terminal. I 
also tried modifying the .cshrc file to add the directory to the PATH 
manually, but it still will not stick after rebooting. 
freesurfer-linux-centos7_x86_64-7.4.1-20230613-7eb8460 Setting up 
environment for FreeSurfer/FS-FAST (and FSL)FREESURFER_HOME   
/usr/local/freesurfer/7.4.1-1FSFAST_HOME       
/usr/local/freesurfer/7.4.1-1/fsfastFSF_OUTPUT_FORMAT nii.gzSUBJECTS_DIR   
   /usr/local/freesurfer/7..4.1-1/subjectsMNI_DIR     
      /usr/local/freesurfer/7.4.1-1/mniFSL_DIR     
      /usr/local/FSL/fsl_6_0_7_4[cogdmd@cari6 
~]$ Thanks,Eddie#umask
 002setenv PATH /usr/local/cuda-9.1/bin:$PATHsetenv LD_LIBRARY_PATH 
/usr/local/cuda-9.1/lib64# auto-inserted by @update.afni.binaries :set path = ( 
$path  /home/cogdmd/abin  ) setenv R_LIBS ~/R#FSL Setupsetenv 
FSLDIR /usr/local/FSL/fsl_6_0_7_4setenv PATH 
${FSLDIR}/share/fsl/bin:${PATH}source ${FSLDIR}/etc/fslconf/fsl.csh#Freesurfer 
Setupsetenv FREESURFER_HOME /usr/local/freesurfer/7.4.1-1setenv SUBJECTS_DIR 
$FREESURFER_HOME/subjectssource $FREESURFER_HOME/SetUpFreeSurfer.cshalias spm12 
'matlab -r "addpath /usr/local/SPM/spm12_r7771/spm12; spm fMRI"'alias conn 
'matlab -r "addpath /usr/local/SPM/spm12_r7771/spm12; addpath 
/usr/local/SPM/conn; conn"'setenv PATH /home/cogdmd/anaconda3/bin:$PATHsetenv 
ANTSPATH /home/cogdmd/ants-2.4.1/binsetenv PATH ${ANTSPATH}:${PATH}setenv PATH 
/home/cogdmd/.lcmodel:$PATH-- Edward
 A. ZunigaSenior Research AnalystVirginia Commonwealth UniversityC. Kenneth and 
Dianne Wright Center for Clinical and Translational ResearchInstitute for Drug 
and Alcohol StudiesCollaborative Advanced Research Imaging (CARI) Facility203 
East Cary Street, Suite 202Richmond, Virginia 23219Phone: (804) 828-4184Fax: 
(804) 
827-2565eazuniga@vcu.edu___Freesurfer
 mailing 
listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail.

[Freesurfer] fRe: SAMSEG lesion mask pattern on Mac with M2 processor and GPU

2023-10-07 Thread fsbuild

External Email - Use Caution

 Python code  (including 3rd party python packages) in the Intel Mac 
build cannot be guaranteed to run on Mac M1, M2 arm processors.  Package 
developers may still build their code using Intel processor specific 
instructions which cannot be emulated by the Rosetta environment on arm64 Macs. 
 Rosetta translates Intel processor instructions to arm64 processor 
instructions; when there is no equivalent arm processor instruction, you get 
the error “illegal instruction”.  The remedy for this is to re-write 
and/or re-build the code (to be more portable).
There is an arm64 freesurfer development build including an arm64 python with 
Apple’s tensorflow.   However, the freesurfer python code is not yet 
entirely compatible with arm64 python and all its packages.  The 
mri_synthsr script currently does not work with arm64 tensorflow; I don’t know 
about mri_samseg.   You can try the arm64 development build via the link, 
 https://secure-web.cisco.com/17oMRv7D8FpOpyCTDI2b6q3ZFH9-liuuaw55Fk0qAsqgBnL3cDmnkVAujZjuxE5eX79DEYS-N-28sS2kPCHZELA_TD9KfXA1gTpkIIQlltrdLjmUYAErTEyV7pXp61dNngBidguhX9Ro7dWKp68cyGlPyIUMglyRLC5Ic8KxVhEd1h6taIbJUs2RF62qX_akkZQzboTafybXKGqtqZO75VJ_VYmF1FbMwq5IEVXbxaM1fZtZ1ZQn6V7EGFGVpOnhJcYCh6SCvDAdGOF8jbC_XE4GUihNWJa4hRA4860MsPxHxc4Or__ON8TElFES-SLctaTntlZ16qO5C18SyRBuAGw/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Fpub%2Fdist%2Ffreesurfer%2Fdev%2Ffreesurfer-macOS-darwin_arm64-dev.pkg%26nbsp;
 Please keep in mind this it not a release build and please report any errors.
Fixes for these kinds of issues will become available in the development builds 
via the link above once they are added into the freesurfer development 
stream.   We can also notify the list.
- R.
On Oct 7, 2023, at 03:23, Bianka Forgó  
wrote:External Email - Use 
CautionDear Freesurfer 
Developers,I am attempting to use Freesurfer on MacOS Ventura (version 13.5.2) 
with an M2 Pro silicone chip and GPU. I have successfully installed Freesurfer 
version 7.4.1.I am trying to use samseg for cross-sectional MS lesion 
volume analysis by running the following command:run_samseg --input 
Freesurfer_subjects/T1.nii Freesurfer_subjects/FAMUS/T2FLAIR_reg.nii 
--pallidum-separate --lesion --lesion-mask-pattern 0 1 --output 
Freesurfer_subjects/FAMUS/samsegI get the error message:zsh: illegal hardware 
instruction  run_samseg --input 
Freesurfer_subjects/FAMUS/T1.nii   --lesion  0 
1 As described in the samseg manual, one may be prompted to use 
Tensorflow when using this module for the first time. I was not prompted to do 
so but I did install it (and python3 as well) using the instructions 
here: MailScanner has detected a possible fraud attempt from 
"secure-web.cisco.com" claiming to 
be https://secure-web.cisco.com/1tE2yZiNK2sSgfXl2g2jsBKvz4UwOnAafBZo84FMcVUl1GYayXd0hNDmJphJPV5PjstNU56Mv2-ZHz2gHhAMlXY3hWsiVC1FHjeMi3zwh2v7t_xAJuVou-EfEHo44tHTgbXtjVRgAo0DpLGaC8q50HrjvkQVVyuN6wNvj4caVEzxRrcejp5Id1tZxys3U7RcpxmayW_RhSEZaQHfCJ1Q1oyXrUi1TDf4yT6v1xP-orC4T-AL7A03jXfucvl8wdsmShOubje1GwxXexAM8kDz2tCP3gurL_HfDY8e92Qv3usVI1_utdRBWx-wdHAUfywhLR6tzDc_UhJgGLNgh0-ILoA/https%3A%2F%2Fwww.tensorflow.org%2Finstall%2FpipAfter
 this, I still get the above error message.I can also see that there is no 
support for running Tensorflow on Mac with GPU.Does this mean that there's 
no way for me to run this command or is there anything else I can try to solve 
this?Of note, the basic samseg command (run_samseg --input 
 [ ...] --output  [--threads 
] [--pallidum-separate]) is running without any 
issues.Thank 
you,Bianka___Freesurfer mailing 
listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail.

Re: [Freesurfer] segmentThalamicNuclei.sh and Matlab Runtime

2023-10-04 Thread fsbuild

External Email - Use Caution


Try setting DYLD_LIBRARY_PATH to point to the subdirectories containing the 
Matlab libraries.



You could just delete what's there,



$ export FREESURFER_HOME=/Applications/freesurfer/7.3.2

$ cd $FREESURFER_HOME

$ sudo rm MCRv97



- and re-run fs_Install_mcr,



$ cd  bin

$ sudo FREESURFER_HOME=$FREESURFER_HOME ./fs_install_mcr R2019b



 the script should output the paths to the subdirectories with the 
libraries to add to DYLD_LIBRARY_PATH at the end of it output.  



On the target computer, append the following to your DYLD_LIBRARY_PATH 
environment variable:

  

/var/folders/yy/abc/install-target/v97/runtime/maci64:/var/folders/yy/abc//install-target/v97/sys/os/maci64:/var/folders/yy/abc/install-target/v97/bin/maci64:/var/folders/abc/install-target/v97/extern/bin/maci64

  

If MATLAB Runtime is to be used with MATLAB Production Server, you do not need 
to modify the above environment variable.




The paths listed for your machine will be different compared to the 
above, but just copy and paste what is listed for the entire series 
of paths into the command,



$ export 
DYLD_LIBRARY_PATH=$DYLD_LIBRARY_PATH:/var/folders/yy/abc/install-target/v97/runtime/maci64:/var/folders/yy/abc//install-target/v97/sys/os/maci64:/var/folders/yy/abc/install-target/v97/bin/maci64:/var/folders/abc/install-target/v97/extern/bin/maci64



- R.





On 10/3/23 21:35, Iglesias Gonzalez, Juan E. 
(jiglesiasgonza...@mgh.harvard..edu) wrote:







  External Email - Use 
Caution

  
Dera Lauren,
I am a bit confused: is /Applications/freesurfer/7.3.2/MCRv97 pointing to
 /Applications/MATLAB/MATLAB_Runtime/R2019b/MCRv97?
Cheers,
/Eugenio
 


--
Juan Eugenio Iglesias


http://secure-web.cisco.com/1bqVymEumCTwxGQGbfGgRiZlYNLDyBIOW6zSN5FfiWaLUE4avNpS5ndTC_b-lmKjfuDeqfShAhvKEUUBtern_Sf4_Pck3lqfmued-BBIGDQxMxombrQVSz6We941VmXiva7eATA-sFLDzlhGA9SUj-WUv8uTsOQR6F8B9fLkdO9awXdEGopzCxm_xUh-KEmrrnwtQMclAUB3BkuTGoP6IVhuJLHqwGO5B2XJ1EMjailflpgVXZ7scfYxdZehoC1eTc3rSstLQja84-HM5dq_UpKR6qG9Gc4kIjvcUTdjDYNlw03lxL8AFFcWJ1D9wMU6L/http%3A%2F%2Fwww.jeiglesias.com
 



From:
freesurfer-boun...@nmr.mgh.harvard.edu
  on behalf of Lauren 
Stephens 

Date: Tuesday, October 3, 2023 at 1:23 PM

To: freesurfer@nmr.mgh.harvard.edu 

Subject: [Freesurfer] segmentThalamicNuclei.sh and Matlab Runtime

External Email - Use 
Caution

Hi FreeSurfers, 


 


I have been attempting to run segmentThalamicNuclei.sh and continue 
getting the error: 


 


ERROR: cannot find Matlab 2019b runtime in location:
     
/Applications/freesurfer/7.3.2/MCRv97
     
It is looking for either: 
 
bin/glnxa64/libmwlaunchermain.so   
(Linux 64b) or
 
bin/maci64/libmwlaunchermain.dylib (Mac 64b)
 
The hippocampal/amygdala and brainstem modules require the (free) Matlab 
runtime.
You will need to download the Matlab Compiler Runtime (MCR) for Matlab 2019b.
To do so, please run the following command (you might need root permissions):
 
fs_install_mcr R2019b
 
For further details, please visit 
https://secure-web.cisco.com/1ECsrk1Jpk7yzuD5ZaV9DNMKMMh3AzKfgXjXeiMKyBiQtU_0DDobyuRoXd5tik5QQw16SItCVsu1pBM7Nyc8Ub42HJuMZdpFFq-4iYV2ww0gK-7eR3ysbWlrca7QgQKSHo6N2HDKRvVylQB4Cm8LHtLAv6WZKbhKhz4f4kgj3cM3-F8Ht_vQpY12KzyhZa4Mmyx4vJ3i_LA23EXpLaBLCYX8Tgk1iIdgolNHULemQK5m_kWFSr5sYROwoMsvR1QlT5yIXs5GP0wxcfH7-L77-Y6B-dPHQlDkCSjPufnJpVeyos6410wv-Ql-q14gsAsUm3Eqxn83xh-_1SWr_5iLlCQ/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FMatlabRuntime
Current path setup on our Mac: /Applications/freesurfer/7.3.2/MCRv97


 


Symbolic
 link setup on our Mac named 
MCRv97: /Applications/MATLAB/MATLAB_Runtime/R2019b/MCRv97/bin/maci64/libmwlaunchermain.dylib 


 


However,
 I have already installed the runtime and have alternatively created a 
symbolic link with Matlab we already have installed on our Mac.  



I have also confirmed the runtime file exists on the machine 

ln: MCRv91/MATLAB_R2016b.app: File exists




 
We are using FreeSurfer version 7.3.2 on an iMac Pro with Ventura 
13.6.  
 
Any suggestions for how to get the matlab runtime issue resolved in order to 
reun the segmentThalamicNuclei.sh code.  
 
Thank you, 
 
Lauren Stephens
 

Lauren Stephens, MS 
Assistant Clinical Research Coordinator 
Department of Psychiatry and Behavioral Science 
Stanford University School of Medicine  
E: laure...@stanford.edu 
P: (650)-725-1716
 





  




  

  
  ___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://secure-web.cisco.com/1LxpoMnV5h1f2ygJQboSTSQlVwoERVFIH7w5Ps1dKObSS94rUjGLND-mVqCHmmIFNBSJ1qGkZOf_wc0-HxSW3Aja5cX3powe0M8YwVcZYcQLilZrMoj9mRrL8IiGcNPqlD7_7-5SbkhDBhx-dZQCYldHqFnF9krTH_WDFf3PLrnFihvCDB_F3MRe160vykqPyJRKXP1LnkQzMXOiDYhalNwXNGilMHwOaKtTRPE7JLRRKhKlkke7r4ZTmJnxRLSif0ElGFVSuJiLLyToZmmf3mHW-q0YbBg_umCMMrGVPS1j_Sn6XA6C7JqZcUmRSYmJFxrSzPpDP4zm5uaZEdhFkjg/h

Re: [Freesurfer] Free surfer quits unexpectedly

2023-10-03 Thread fsbuild

External Email - Use Caution

 Please try the following,
… open a new terminal and run the bash shell … I am cd’d to /tmp though it 
should not matter ...
$ cd /tmp$ bashThe default interactive shell is now zsh.To update your account 
to use zsh, please run `chsh -s /bin/zsh`.For more details, please visit 
https://secure-web.cisco.com/1B3JRrCA1-GeI0tKc8qR9oVMx4vfk7xlYLxiqqBDOBuaesSZHdUEoF9qZ0tWGzGysXuBCEyOpSbXvD_sNqeR-owCXvQsiqm26_9KLalRHeelYHSZQBpacOtpGfPVqO2KTCVR22uzOtp0zFueNRfCITldF6fv-mcOBUheFxV8vLVqr5iTe-nNcq-6ZOaO8MmiDu8oUjdUVLpxwzSYpD7qFV5luFGQ4DYq8YkJAn22_0_I3m84W7sEZDUljCB3QSXifOAvmqyywNPtjdCj0KDvfgVqz6baSBBPtmmLdIsDSaBjYPJUA4i_PCdquW0cDjNybWB8c9JsJOtj_SYkg2acvvg/https%3A%2F%2Fsupport.apple.com%2Fkb%2FHT208050
… check the version of Quartz by starting an xterm.  When the xterm 
window opens check the version from the upper left hand corner XQuartz 
application pull down menu and check what “About X11” reports.  Check 
you have Quartz 2.8.2 or later and then quit the xterm window.
Mac:/tmp> which xterm/opt/X11/bin/xtermMac:/tmp> xterm &
… copy your license.txt file into your home directory.  For example 
if you downloaded the license by default into your Downloads folder, then copy 
it from there into $HOME …
Mac:/tmp> cd $HOMEMac:~> cp -p -f ./Downloads/license.txt .
… set the environment variable FS_LICENSE to point to the license file … later 
you can put this in your shell init file to be the default when you launch a 
new terminal window with your default shell … 
Mac:~> export FS_LICENSE=$HOME/license.txtMac:~> head -1 
$fs_license...@somedomain.com             
      <— email you used to register for the license
… setup the freesurfer environment …
Mac:~> export 
FREESURFER_HOME=/Applications/freesurfer/7.4.1Mac:~> source 
$FREESURFER_HOME/SetUpFreeSurfer.sh 
freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 Setting up 
environment for FreeSurfer/FS-FAST (and 
FSL)FREESURFER_HOME   /Applications/freesurfer/7.4.1FSFAST_HOME  
     /Applications/freesurfer/7.4.1/fsfastFSF_OUTPUT_FORMAT 
nii.gzSUBJECTS_DIR    
  /Applications/freesurfer/7.4.1/subjectsMNI_DIR     
      /Applications/freesurfer/7.4.1/mni
… first check freeview with no arguments opens an empty window …
Mac:~>  which 
freeview/Applications/freesurfer/7.4.1/bin/freeviewMac:~> freeview
… close the freeview window and try to open a knoen to be good volume file ...
… check the volume file exists …
Mac:~> ls -l $SUBJECTS_DIR/bert/mri/T1.mgz-rwxr-xr-x  1 
root  wheel  4502402 Jul 13  2021 
/Applications/freesurfer/7.4.1/subjects/bert/mri/T1.mgz*
… try opening the volume file …Mac:~> freeview 
$SUBJECTS_DIR/bert/mri/T1.mgz
If the above works try opening one of your own volume or surface files.
BTW - you should update MacOS on your machine from 12.6.7 to 12.7 as there are 
important security fixes in 12.7.
- R.
On Oct 4, 2023, at 00:53, Clara Massaneda Tuneu 
 
wrote:External Email - Use 
CautionHi, I'm attempting 
to install and run FreeSurfer, but every time I try to load data, the program 
unexpectedly quits. I downloaded the license from the email sent by FreeSurfer 
and followed the instructions of the video tutorial. I've also downloaded 
and installed the latest version of XQuartz before installing and executing 
FreeSurfer. When I tried to open FreeView in my terminal and load the image, 
there was no message in my terminal explaining why the program 
crashes. The version of FreeSurfer that I'm using is 
freesurfer-macOS-darwin_x86_64-7.4.1. My device is a MacBook Pro (2016) running 
version 12.6.7, with a 2 GHz Dual-Core Intel Core i5 processor and 8GB of 
memory. I've searched the list, and no similar errors have been reported. 
Does anyone have any thoughts on how to troubleshoot this issue? Thanks 
for your help.  Clara 
MT___Freesurfer mailing 
listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail.

1 2 3 4 5 6 7 >

1 - 100 of 631 matches

Mail list logo