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

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

[Tran, Kevin (NIH/NIMH) [E]]

External Email - Use Caution

Hi,
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 Tran
Data Scientist
The National Institutes of Health
NIMH, Laboratory of Brain and Cognition
10 Center Drive, Room 4C215
Bethesda MD 20892-1366
kevint...@mail.nih.gov
Work:(301)435-4936 Cell:(301)755-3715
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Re: [Freesurfer] Help with Recon-all Errors

[Silvia De Francesco]

External Email - Use Caution

unsubscribe 


From: "Perumalla, Sucika"  
To: "freesurfer"  
Sent: Wednesday, February 21, 2024 4:30:39 PM 
Subject: [Freesurfer] Help with Recon-all Errors 

Questa è la prima volta che ricevi un'email da questo mittente. Assicurati che 
sia qualcuno di cui ti fidi. 


Hello FreeSurfer Support, 



My name is Sucika Perumalla and I hope you can please help me with 
troubleshooting recon-all. I’m getting multiple frames errors when trying to 
run recon-all with my dicoms even after extracting the multiple frames. I was 
wondering if you can please help resolve this issue. Please refer to the 
attachment with my recon-all log. 



Thanks 


_ 

Sucika Perumalla 

Clinical Research Assistant I 

Department of Neurology, Division of Movement Disorders 

Brigham and Women’s Hospital 

60 Fenwood Road, Boston, MA 02115 

[ mailto:sperumal...@bwh.harvard.edu | sperumal...@bwh.harvard.edu ] | 
508-414-2601 




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[Freesurfer] Help with Recon-all Errors

[Perumalla, Sucika]

Hello FreeSurfer Support,

My name is Sucika Perumalla and I hope you can please help me with 
troubleshooting recon-all. I’m getting multiple frames errors when trying to 
run recon-all with my dicoms even after extracting the multiple frames. I was 
wondering if you can please help resolve this issue. Please refer to the 
attachment with my recon-all log.

Thanks
_
Sucika Perumalla
Clinical Research Assistant I
Department of Neurology, Division of Movement Disorders
Brigham and Women’s Hospital
60 Fenwood Road, Boston, MA 02115
sperumal...@bwh.harvard.edu | 508-414-2601

Last login: Tue Feb 20 11:15:44 on ttys001
sucikaperumalla@PHS027570 ~ % 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
sucikaperumalla@PHS027570 ~ % export 
DATA=/Applications/freesurfer/7.4.1/subjects/JacquelineOneill/E36409769
sucikaperumalla@PHS027570 ~ % cd $DATA
sucikaperumalla@PHS027570 E36409769 % recon-all -s JO1 -i 
/Applications/freesurfer/7.4.1/subjects/JacquelineOneill/E36409769/Ax_T1_3D_MPRAGE/765855840.dcm
 -all -qcache
fs-check-version --s JO1 --o 
/var/folders/j5/20t8sd891y5_z4_q07d5b2kmgr/T//tmp.wTf2uk
Tue Feb 20 11:25:01 EST 2024

setenv SUBJECTS_DIR /Applications/freesurfer/7.4.1/subjects
cd /Applications/freesurfer/7.4.1/subjects/JacquelineOneill/E36409769
/Applications/freesurfer/7.4.1/bin/fs-check-version --s JO1 --o 
/var/folders/j5/20t8sd891y5_z4_q07d5b2kmgr/T//tmp.wTf2uk
-rwxrwxrwx  1 root  wheel  18565 Jun 14  2023 
/Applications/freesurfer/7.4.1/bin/fs-check-version

freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460
$Id$
Darwin PHS027570 23.2.0 Darwin Kernel Version 23.2.0: Wed Nov 15 21:53:18 PST 
2023; root:xnu-10002.61.3~2/RELEASE_ARM64_T6000 arm64
pid 4595
Current FS Version freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460
Subject does not have a bstampfile, copying 
/Applications/freesurfer/7.4.1/build-stamp.txt
Subject FS Version: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460
No constraints on version because REQ=UnSet and FsVerFile=NotThere
#@#% fs-check-version match = 1
fs-check-version Done
INFO: SUBJECTS_DIR is /Applications/freesurfer/7.4.1/subjects
Actual FREESURFER_HOME /Applications/freesurfer/7.4.1
Darwin PHS027570 23.2.0 Darwin Kernel Version 23.2.0: Wed Nov 15 21:53:18 PST 
2023; root:xnu-10002.61.3~2/RELEASE_ARM64_T6000 arm64
/Applications/freesurfer/7.4.1/subjects/JO1
\n mri_convert 
/Applications/freesurfer/7.4.1/subjects/JacquelineOneill/E36409769/Ax_T1_3D_MPRAGE/765855840.dcm
 /Applications/freesurfer/7.4.1/subjects/JO1/mri/orig/001.mgz \n
mri_convert 
/Applications/freesurfer/7.4.1/subjects/JacquelineOneill/E36409769/Ax_T1_3D_MPRAGE/765855840.dcm
 /Applications/freesurfer/7.4.1/subjects/JO1/mri/orig/001.mgz 
reading from 
/Applications/freesurfer/7.4.1/subjects/JacquelineOneill/E36409769/Ax_T1_3D_MPRAGE/765855840.dcm...
mriio.cpp: starting DICOMRead3()
Starting DICOMRead3()
dcmfile = 
/Applications/freesurfer/7.4.1/subjects/JacquelineOneill/E36409769/Ax_T1_3D_MPRAGE/765855840.dcm
dcmdir = 
/Applications/freesurfer/7.4.1/subjects/JacquelineOneill/E36409769/Ax_T1_3D_MPRAGE
Found 384 DICOM file(s)
load Image 
/Applications/freesurfer/7.4.1/subjects/JacquelineOneill/E36409769/Ax_T1_3D_MPRAGE/765855821.dcm,
 size 114688
Warning: Unable to determine slice direction: please check whether slices are 
flipped
Warning: Unable to determine slice direction: please check whether slices are 
flipped
Convert 384 DICOM (224x256x192x2)
DICOM row order preserved: may appear upside down in tools that ignore spatial 
transforms
WARNING: MRIsetRas2VoxFromMatrix(): voxels sizes are inconsistent
   (0.976562,0.976562) (0.976562,0.976562) (1,0) 
This is probably due to shear in the vox2ras matrix
Input Vox2RAS --
-0.97656   0.0  -0.0   105.30721;
-0.0  -0.97656  -0.0   122.96610;
 0.0   0.0   0.0  -113.12712;
 0.0   0.0   0.0   0.0;
TR=2000.00, TE=3.03, TI=1100.00, flip angle=15.00
i_ras = (-1, -4.897e-12, 0)
j_ras = (4.897e-12, -1, 0)
k_ras = (nan, nan, nan)
writing to /Applications/freesurfer/7.4.1/subjects/JO1/mri/orig/001.mgz...
#
#@# MotionCor Tue Feb 20 11:25:45 EST 2024
Found 1 runs
/Applications/freesurfer/7.4.1/subjects/JO1/mri/orig/001.mgz
Checking for (invalid) multi-frame inputs...
ERROR: input(s) cannot have multiple frames!
/Applications/freesurfer/7.4.1/subjects/JO1/mri/orig/001.mgz has 2 frames
Darwin PHS027570 23.2.0 Darwin Kernel Version 23.2.0: Wed Nov 15 21:53:18 PST 
2023; 

Re: [Freesurfer] Help Download FreeSurfer Windows VM

[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

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 .
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[Freesurfer] Help Download FreeSurfer Windows VM

[lioudadracacci]

   External Email - Use Caution


Hello 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
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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 
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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 transform matrix for SEEG

[Douglas N. Greve]

Have you seen this page 
https://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems ?


On 12/10/2023 8:55 AM, Hyunchul Lee wrote:


External Email - Use Caution

Hello,
I've just started using Freesurfer this week and I'm quite confused 
about coordinate systems.
Specifically, I have SEEG electrode locations that have been digitized 
in MRI RAS space, and I'm trying to apply a transform matrix so that 
these electrodes will be registered with the same brain that I 
performed recon-all on using Freesurfer, so that I can do further 
analysis in MNE python.


I understand that voxel space to MRI RAS space transform matrix is 
stored in vox2ras and the transform for voxel space to Freesurfer's 
surface RAS is in vox2ras_tkr of T1.mgz in my subject folder. Since 
the electrodes are in MRI RAS space, I am applying a transform matrix 
that is a matrix product of inverse(vox2ras) and vox2ras_tkr. However, 
this doesn't work out in real life, and I end up with electrodes half 
way outside the head.


Am I using the correct matrices? Also, T1.affine appears similar to 
vox2ras but very slightly different. Just hoping that there would be 
an easier way..

Best regards,
*
*
*Hyunchul Lee*  MBBS PhD

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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 
 .

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

[Kiyotaka Nemoto]

External Email - Use Caution

Dear R,

Thank you for the information. The deb package is useful so I agree with
you. Only one point is that using deb cannot handle installing two
different versions. Do you have any recommendation managing two (or more)
different versions using deb package?

Best regards,

Kiyotaka


On Sat, Dec 30, 2023 at 1:21 PM fsbuild  wrote:

> 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  wrote:
>
> External Email - Use Caution
>
> Dear 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,
>
> Kiyotaka
>
> sudo 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  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 be*
>> https://secure-web.cisco.com/1J9_Z0HLKDYWwXrGPXi_fqFTQLygJlwVaU-141E5zzDhAkkw1xXapN0nnVgWhTS6XGCgfkc5ueirEA_jvddWCTdYAfUcAH7SxCSaFAzawZC4lvbC8y_9NKqsjhD5ZFMrWt7X3muEEOwu9TlGI9rdd8dbC5nuG2Ghq2KLE70SI4ZxUWWmXSVkXCZyhhXZq5f4wFQyAvLrAHPX0lR7gws9mQ_Q3UYrjc-3musq7AJqT7K0xWCpNBXEO5jRyNhN_5IQyFWAx8la8y0nyTkV52oB8n6sf4nY9sqgm_KaTMe8Mr5-hIcABk8sdULBQpIZmVLKy5JEVPha5YlG51rCIN7H38g/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Fpub%2Fdist%2Ffreesurfer%2F7.4.1%2Ffreesurfer_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.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 Caution
>>
>> I 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 list
>> Freesurfer@nmr.mgh.harvard.edu
>> *MailScanner has detected a possible fraud attempt from
>> "secure-web.cisco.com" claiming to be*
>> 

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

[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 ifyou 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 
zlib1gOn Fri, Dec 29, 2023 at 12:14 PM fsbuild 
fsbu...@contbay.com 
wrote:External Email - Use 
CautionThat 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 linkMailScanner 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.deband
 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 tararchive 
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 beinitialized. 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

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

[Kiyotaka Nemoto]

External Email - Use Caution

Dear 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,

Kiyotaka

sudo 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  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 be*
> https://secure-web.cisco.com/1mKMabUX5OEUvCDYuNLL03gy4wla33dNI6Ox8dPzZ_qBoLFWXoufcqAf2xdwBE_BLgKkXD80OQ5NgOUxywRL0N0wr63y6xGFPMuYMVhScIysNXav0Y4z28Z__cNw9SgCGUW68fdgfU8QDsRvR5NNF7vdpsshn6ACHPjYJr6JQcf2sCXJjoGxWj4hC7KyiUOhaRHIYOptZ1d1TMm10pJl2Wo80JxmbN_ExW9WtWOeJE3QcI24nX9nwDsHhamhR7k-K7nlz_WIGFKPWcZpmd9U4iSiiuAC41kYHaqh3oc15rOX9GB1n5yIcEKNHfnxbQ8Q_Pl7T-Cii52ogXtnRAF4Nnw/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Fpub%2Fdist%2Ffreesurfer%2F7.4.1%2Ffreesurfer_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.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 Caution
>
> I 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 list
> Freesurfer@nmr.mgh.harvard.edu
> https://secure-web.cisco.com/1QI73ha0dZUxEGvYoEY_1bYLyCUQHOXV-uF3VAAGaEPKSzyD1nk2DxAarPrXJTqvTusR8gBzTyWOW2-kKzsxSeIadM-y30LBoFcSz5mxwl6BrxdQ6Inv507a1TZr765rV_NZR-bk698jbJ-vqcPvC4EKJ5UTWDndvRP0uBpApG-TtOsQUPPG8ZHqP6nuQ0_aya37i0g22_g_ZxtO8xo3uJ7k-zPCumS_Eh5wFjz0kMaNw8xK2i_tLxfm9uND_vZiF4BA8RBWhfWCKe3bjJxORg6txWtP7nqolZUOmiK8132YcfTy76x54nkehXXP1lKggt5vEVxPG3qW4ilDrAduriw/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://secure-web.cisco.com/1QI73ha0dZUxEGvYoEY_1bYLyCUQHOXV-uF3VAAGaEPKSzyD1nk2DxAarPrXJTqvTusR8gBzTyWOW2-kKzsxSeIadM-y30LBoFcSz5mxwl6BrxdQ6Inv507a1TZr765rV_NZR-bk698jbJ-vqcPvC4EKJ5UTWDndvRP0uBpApG-TtOsQUPPG8ZHqP6nuQ0_aya37i0g22_g_ZxtO8xo3uJ7k-zPCumS_Eh5wFjz0kMaNw8xK2i_tLxfm9uND_vZiF4BA8RBWhfWCKe3bjJxORg6txWtP7nqolZUOmiK8132YcfTy76x54nkehXXP1lKggt5vEVxPG3qW4ilDrAduriw/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer



-- 
Kiyotaka Nemoto, M.D., Ph.D.
Associate Professor
Department of Psychiatry
Division of 

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

[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 
linkhttps://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 jorrydep9...@gmail.com 
wrote:External Email - Use 
CautionI have installed 
FreeSurfer 7.4.1 on Ubuntu 22.04 using the binary tararchive 
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 beinitialized. 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

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[Freesurfer] Help (Freeview fails to launch)

[Akira Kita]

External Email - Use Caution

I 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
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[Freesurfer] Help with transform matrix for SEEG

[Hyunchul Lee]

External Email - Use Caution

Hello,
I've just started using Freesurfer this week and I'm quite confused about
coordinate systems.
Specifically, I have SEEG electrode locations that have been digitized in
MRI RAS space, and I'm trying to apply a transform matrix so that these
electrodes will be registered with the same brain that I performed
recon-all on using Freesurfer, so that I can do further analysis in MNE
python.

I understand that voxel space to MRI RAS space transform matrix is stored
in vox2ras and the transform for voxel space to Freesurfer's surface RAS is
in vox2ras_tkr of T1.mgz in my subject folder. Since the electrodes are in
MRI RAS space, I am applying a transform matrix that is a matrix product of
inverse(vox2ras) and vox2ras_tkr. However, this doesn't work out in real
life, and I end up with electrodes half way outside the head.

Am I using the correct matrices? Also, T1.affine appears similar to vox2ras
but very slightly different. Just hoping that there would be an easier
way..
Best regards,

*Hyunchul Lee*  MBBS PhD
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Re: [Freesurfer] Help

[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 Wuxlw...@groton.orgReply-To:Freesurfer 
support 
listfreesurfer@nmr.mgh.harvard.eduTo: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,LucasAttached Message Part.txt

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[Freesurfer] Help

[Xincen Wu]

External Email - Use Caution

Hi,

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 -autorecon1

an 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
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continue to communicate over unencrypted e-mail. 

Re: [Freesurfer] Help running freesurfer for FEAT-preprocessed functional data?

[Douglas N. Greve]

   External Email - Use Caution

There is no way to do this. All the fsfast commands are going to expect 
things to be in the fsfast directory structure.


On 8/11/2023 12:19 PM, Noah Lee wrote:


External Email - Use Caution

Hello!

I am trying to run some freesurfer commands for a pipeline. However, I 
am coming in with functional data preprocessed by FEAT (EPI correction 
and general mcflirt, etc). For reference, I'm trying to run this 
following script:


preproc-sess -s . -fwhm 5 -stc siemens -surface fsaverage lhrh 
-per-run -fsd bold -mni305 -force

fcseed-config -wm -fcname wm.dat -fsd bold -mean -cfg wm.config -force
fcseed-config -vcsf -fcname vcsf.dat -fsd bold -mean -cfg vcsf.config 
-force

fcseed-sess -s . -cfg wm.config -force
fcseed-sess -s . -cfg vcsf.config -force

I am obviously skipping the preproc-sess step, as my data has been 
preprocessed. However, I'm not too sure how to run the following steps 
with the outputs of my feat directory. If anyone could help, I would 
greatly appreciate it!


Best,

Noah Lee
he/him/his
Yale University | Saybrook '25
B.S. Neuroscience


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[Freesurfer] Help running freesurfer for FEAT-preprocessed functional data?

[Noah Lee]

External Email - Use Caution

Hello!

I am trying to run some freesurfer commands for a pipeline. However, I am
coming in with functional data preprocessed by FEAT (EPI correction and
general mcflirt, etc). For reference, I'm trying to run this following
script:

preproc-sess -s . -fwhm 5 -stc siemens -surface fsaverage lhrh -per-run
-fsd bold -mni305 -force
fcseed-config -wm -fcname wm.dat -fsd bold -mean -cfg wm.config -force
fcseed-config -vcsf -fcname vcsf.dat -fsd bold -mean -cfg vcsf.config -force
fcseed-sess -s . -cfg wm.config -force
fcseed-sess -s . -cfg vcsf.config -force

I am obviously skipping the preproc-sess step, as my data has been
preprocessed. However, I'm not too sure how to run the following steps with
the outputs of my feat directory. If anyone could help, I would greatly
appreciate it!

Best,

Noah Lee
he/him/his
Yale University | Saybrook '25
B.S. Neuroscience
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Re: [Freesurfer] Help Needed with Thalamic NucleiDTI Module and Freeview Display

[Tregidgo, Henry]

External Email - Use Caution

Hi,

Thank you for your interest in our tool. Currently these three nuclei are not 
segmented by the network implementation, but they will be segmented by the 
Bayesian tool once we have integrated it into FreeSurfer.

The Pc, VM and Pt are the three smallest nuclei in our atlas, with volumes 
generally less than 2-3 mm^3. As such they often do not have the highest 
posterior probability in any voxels during Bayesian segmentation and therefore 
don't appear in the output segmentations or only in very few voxels. We 
therefore decided to remove these labels when training the network 
implementation.

To view the segmentations you can use the following command substituting the 
paths for the segmentation, V1, FA and aligned T1 volumes

freeview  :colormap=LUT -dti  


Best wishes,
Henry


Henry Tregidgo, PhD
Research Associate

Centre for Medical Image Computing (CMIC),
University College London (UCL)



From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of 胡馨月 
Sent: 18 May 2023 13:15
To: freesurfer@nmr.mgh.harvard.edu 
Subject: [Freesurfer] Help Needed with Thalamic NucleiDTI Module and Freeview 
Display


⚠ Caution: External sender


External Email - Use Caution

Dear FreeSurfer Experts,

I hope you are doing well. I have encountered an issue while using the Thalamic 
NucleiDTI module in FreeSurfer and would appreciate your guidance.

I am attempting to segment the thalamus using the module, but the Pc, VM, and 
Pt nuclei are missing in the segmentation results. Could you please advise me 
on resolving this issue?

Additionally, I would like instructions on how to display the Thalamic 
NucleiDTI module results in Freeview. Please guide me on the steps to visualize 
the results accurately in Freeview.

Thank you for your support. I look forward to your response.

Best regards,

Xinyue Hu West China Hospital of Sichuan University
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[Freesurfer] Help Needed with Thalamic NucleiDTI Module and Freeview Display

[胡馨月]

External Email - Use Caution

Dear FreeSurfer Experts,

I hope you are doing well. I have encountered an issue while using the
Thalamic NucleiDTI module in FreeSurfer and would appreciate your guidance.

I am attempting to segment the thalamus using the module, but the Pc, VM,
and Pt nuclei are missing in the segmentation results. Could you please
advise me on resolving this issue?

Additionally, I would like instructions on how to display the Thalamic
NucleiDTI module results in Freeview. Please guide me on the steps to
visualize the results accurately in Freeview.

Thank you for your support. I look forward to your response.

Best regards,

Xinyue Hu West China Hospital of Sichuan University
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[Freesurfer] Help passcode

[Isra RM]

External Email - Use Caution

Hello FreeSurfer,
Where can I find a passcode to unzip the VW
file FS_7_2_0_ubuntu_18_04_06.ova.7z I have just downloaded?
Thanks
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[Freesurfer] HELP (I don't have the password to unzip on Winrar/7zip)

[Juan Felipe Gaitan Nocua]

External Email - Use Caution

Hello In this email I request help to acquire the password that the
freesurfer requests when wanting to unzip the file. I have followed the
steps for the installation and this problem does not let me continue. I add
that the reason why I will use the program is for research that we are
doing at the National University of Colombia for the biomedicine and
artificial intelligence research seedbed.

Thanks you.
*--*
*Juan Felipe Gaitan Nocua*
*Ingenieria Electronica*
*Estudiante de la Universidad Nacional de Colombia*

-- 
*Aviso legal:* El contenido de este mensaje y los archivos adjuntos son 
confidenciales y de uso exclusivo de la Universidad Nacional de Colombia. 
Se encuentran dirigidos sólo para el uso del destinatario al cual van 
enviados. La reproducción, lectura y/o copia se encuentran prohibidas a 
cualquier persona diferente a este y puede ser ilegal. Si usted lo ha 
recibido por error, infórmenos y elimínelo de su correo. Los Datos 
Personales serán tratados conforme a la Ley 1581 de 2012 y a nuestra 
Política de Datos Personales que podrá consultar en la página web 
http://secure-web.cisco.com/15qd3FEE_9QR8rTmC4t6iMVtYrajvwHFVh-lK8fSxWhU-Eh_Ubm2ceGwgfvG_5PSk-kRIGIf403RYhw1wLOeQi0l85SQZ9Gqd6MxBy02O453DYaIXkkntuhINWhlRv_UsrzLnY2aPlza-Wg760YnLiudP33YRf7wPTQ-B3-DJWfF3uZEt2UCIRL0OoLaM2DYMD4Tzs2HP4Sw5eAOyQe7P1boitCVglsRRyfOM_FrH5eh-E9zbeFaSVYL_zGyalv-Zg7ugY7TDnBOxAW_0XLqIf8UWhmpcscnA9eqJi-iZ42eaNhnm6mfilKzJ6ddEjqsYPfxEoyMlJ8ECOGbg3j-kjA/http%3A%2F%2Fwww.unal.edu.co
 
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 *Las opiniones, informaciones, 
conclusiones y cualquier otro tipo de dato contenido en este correo 
electrónico, no relacionados con la actividad de la Universidad Nacional de 
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Re: [Freesurfer] [FreeSurfer] Help on installation of Freesurfer on Ubuntu 18 on Windows 11

[fsbuild]

External Email - Use Caution


Hello Krystal,



Doing an "upgrade" is fine, but I don't think you want to do a 
"dist-upgrade". Telling the system to upgrade to the distribution 
likely installed something causing the conflict(s) when you tried to install 
the 7.3.2
 release. If you made a snapshot of the VM when you first booted it 
with 7.2.0 installed, then you could revert back to that snapshot. You 
could revert back to any snapshot you made prior to the 
"dist-upgrade". Otherwise, I think you will have to go back and 
make a
 new copy of the VM so that you are starting out with the system from the 
original disk image file.
The I would try,$ sudo apt-get upgrade$ sudo apt-get install 
./freesurfer_ubuntu18-7.3.2_amd64.deb


- R.



On 2/8/23 10:42, Krystal Xiwing Yau (kryst...@hku.hk) wrote:






  External Email - Use 
Caution

  
Dear FreeSurfer users,



I tried to install the newest version of FreeSurfer 7.3.2on ubuntu 
18..04.6 VB Image.



I have run the following commands before installing:



$ sudo apt-get dist-upgrade


$ sudo apt-get upgrade



$ sudo apt-get install ./freesurfer_ubuntu18-7.3.2_amd64.deb

​
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Re: [Freesurfer] Help with script with 7.2 on an HPC

[Huang, Yujing]

Hi Lisa,

You can find information about those scripts here 
https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfieldsAndNucleiOfAmygdala

Executing the corresponding script with the flag -help should provide some 
information too.

Best,

Yujing

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Taylor, Lisa
Sent: Monday, February 6, 2023 6:17 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Help with script with 7.2 on an HPC


External Email - Use Caution
Hi there,

I am trying to update my scripts on our university's HPC but am running into an 
issue. I am not too savvy when it comes to this, so I apologize. My guess is I 
will have to run my old 6.0 script but without the -hippocampal-subfields-T1 
argument in the new 7.2 script that I copied over, but then run the 
'segmentHA_T1.sh' separately? Is there a way to incorporate this script in the 
7.2 script I currently have? Thank you for any help/insight you can give.

Error I get when trying to run my updated 7.2 script:


 $cat slurm-19565158.out



ERROR: the hippocampal subfield module is now in separate scripts:

  segmentHA_T1.sh

  segmentHA_T2.sh

  segmentHA_T1_long.sh

1 of 2 of the scripts used to run freesurfer on the HPC3:


cat freesurfer_template_7.2.sub

#!/bin/bash

#SBATCH --job-name=fs_reconall_subid

#SBATCH -A account

#SBATCH -p user

#SBATCH --nodes=1

#SBATCH --ntasks=1

#SBATCH --cpus-per-task=2

#SBATCH --error=slurm-reconall_subid.err

#SBATCH --mem-per-cpu=18gb



module load freesurfer/7.2.0

xport SUBJECTS_DIR=imagedir

source $FREESURFER_HOME/SetUpFreeSurfer.sh



# run freesurfer

srun ${FREESURFER_HOME}/bin/recon-all -s imagedir/subid -no-isrunning -all 
-hippocampal-subfields-T1 -brainstem-structures -qcache


2 of 2 of the script used to run freesurfer on the HPC3:


cat 7.2_freesurfer_prep_single_subj.sh

#!/bin/sh



# usage: sh freesurfer_prep_from_nii.sh [queue] [account_to_charge] 
[freesurfer_subj_folder]

# [queue] = free | standard

# [account_to_charge] = ltaylor2

# [freesurfer_subj_folder] = This is the subject directory created by 
freesurfer for processing

#



if [[ $# -lt 3 ]] ; then

  echo 'Usage: sh freesurfer_prep_from_nii.sh [queue] [account_to_charge] 
[freesurfer_subj_folder]'

  echo '[queue] = free | standard'

  echo '[account_to_charge] = ltaylor2'

  echo 'PLEASE ONLY USE THE FREE QUEUE UNLESS OTHERWISE INSTRUCTED'a

  echo '[freesurfer_subj_folder] = This is the subject directory created by 
freesurfer for processing'

  exit 0

fi



subids=$3

imagedir=`echo $PWD`



echo $subids



if [ -d freesurfer_sub ]; then

echo directory freesurfer_sub exists ...;

else

  mkdir freesurfer_sub;

fi





for subid in ${subids}; do

sed -e s/subid/${subid}/g -e s/user/${1}/g -e s/account/${2}/g -e 
s#imagedir#${imagedir}#g freesurfer_template_7.2.sub > 
freesurfer_sub/fs_${subid}.sub



cd freesurfer_sub

echo sbatch fs_${subid}.sub

   sbatch fs_${subid}.sub

cd ..

done


Thank you!

Lisa

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continue to communicate over unencrypted e-mail. 

[Freesurfer] Help with script with 7.2 on an HPC

[Taylor, Lisa]

External Email - Use Caution

Hi there,

I am trying to update my scripts on our university's HPC but am running into an 
issue. I am not too savvy when it comes to this, so I apologize. My guess is I 
will have to run my old 6.0 script but without the -hippocampal-subfields-T1 
argument in the new 7.2 script that I copied over, but then run the 
'segmentHA_T1.sh' separately? Is there a way to incorporate this script in the 
7.2 script I currently have? Thank you for any help/insight you can give.

Error I get when trying to run my updated 7.2 script:


 $cat slurm-19565158.out



ERROR: the hippocampal subfield module is now in separate scripts:

  segmentHA_T1.sh

  segmentHA_T2.sh

  segmentHA_T1_long.sh

1 of 2 of the scripts used to run freesurfer on the HPC3:


cat freesurfer_template_7.2.sub

#!/bin/bash

#SBATCH --job-name=fs_reconall_subid

#SBATCH -A account

#SBATCH -p user

#SBATCH --nodes=1

#SBATCH --ntasks=1

#SBATCH --cpus-per-task=2

#SBATCH --error=slurm-reconall_subid.err

#SBATCH --mem-per-cpu=18gb


module load freesurfer/7.2.0

xport SUBJECTS_DIR=imagedir

source $FREESURFER_HOME/SetUpFreeSurfer.sh


# run freesurfer

srun ${FREESURFER_HOME}/bin/recon-all -s imagedir/subid -no-isrunning -all 
-hippocampal-subfields-T1 -brainstem-structures -qcache


2 of 2 of the script used to run freesurfer on the HPC3:


cat 7.2_freesurfer_prep_single_subj.sh

#!/bin/sh


# usage: sh freesurfer_prep_from_nii.sh [queue] [account_to_charge] 
[freesurfer_subj_folder]

# [queue] = free | standard

# [account_to_charge] = ltaylor2

# [freesurfer_subj_folder] = This is the subject directory created by 
freesurfer for processing

#


if [[ $# -lt 3 ]] ; then

  echo 'Usage: sh freesurfer_prep_from_nii.sh [queue] [account_to_charge] 
[freesurfer_subj_folder]'

  echo '[queue] = free | standard'

  echo '[account_to_charge] = ltaylor2'

  echo 'PLEASE ONLY USE THE FREE QUEUE UNLESS OTHERWISE INSTRUCTED'a

  echo '[freesurfer_subj_folder] = This is the subject directory created by 
freesurfer for processing'

  exit 0

fi


subids=$3

imagedir=`echo $PWD`


echo $subids


if [ -d freesurfer_sub ]; then

echo directory freesurfer_sub exists ...;

else

  mkdir freesurfer_sub;

fi



for subid in ${subids}; do

sed -e s/subid/${subid}/g -e s/user/${1}/g -e s/account/${2}/g -e 
s#imagedir#${imagedir}#g freesurfer_template_7.2.sub > 
freesurfer_sub/fs_${subid}.sub


cd freesurfer_sub

echo sbatch fs_${subid}.sub

   sbatch fs_${subid}.sub

cd ..

done


Thank you!

Lisa

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 .
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Re: [Freesurfer] Help: Aparcstats and asegstats not working

[vittal korann]

External Email - Use Caution

Thanks, Yujing!

Happy new year!

I’m wondering what the first line is in your /usr/local/freesurfer/bin/
asegstats2table
/usr/bin/env python

python asegstats2table –subjects … --tablefile …
python /usr/local/freesurfer/bin/asegstats2table –subjects … --tablefile …
- this worked for me.

Your suggestion worked for me, thanks!

With regards
Vittal



On Mon, Jan 2, 2023 at 3:51 PM Huang, Yujing 
wrote:

> Hi Vittal,
>
>
>
> Happy new year!
>
>
>
> I’m wondering what the first line is in your
> /usr/local/freesurfer/bin/asegstats2table. Can you check it by doing ‘head
> /usr/local/freesurfer/bin/asegstats2table’ at the prompt?
>
>
>
> Can you also try the following?
>
> 1. alias python=python2  (as suggested in previous email)
>
> 2. python asegstats2table –subjects … --tablefile …
>
>
>
> Best,
>
>
>
> Yujing
>
>
>
>
>
>
>
> *From:* vittal korann 
> *Sent:* Friday, December 30, 2022 3:56 PM
> *To:* Huang, Yujing 
> *Cc:* Freesurfer support list 
> *Subject:* Re: [Freesurfer] Help: Aparcstats and asegstats not working
>
>
>
> *External Email - Use Caution*
>
> Thanks, Yujing, for your quick response.
>
>
>
> I tried your suggestion as well but the same error keeps appearing.
>
>
>
> $ asegstats2table --subjects Met001_1 Met002_1 Met003_1 Met005_1 Met006_1
> Met007_1 Met008_1 Met009_1 Met012_1 Met013_1 Met015_1 Met016_1 Met017_1
> Met018_1 Met019_1 Met020_1 Met021_1 Met022_1 Met023_1 Met024_1 Met025_1
> Met026_1 Met029_1 Met030_1 Met031_1 Met033_1 Met034_1 TOPIRA004_1
> TOPIRA005_1 TOPIRA012_1 TOPIRA013_1 TOPIRA019_1 TOPIRA021_1 TOPIRA022_1
> TOPIRA024_1 TOPIRA025_1 TOPIRA026_1 TOPIRA027_1 TOPIRA029_1 TOPIRA030_1
> TOPIRA032_1 Tao101_1 Tao103_1 Tao104_1 Tao105_1 Tao106_1 Tao107_1 Tao108_1
> Tao111_1 Tao112_1 Tao113_1 Tao115_1 Tao117_1 Tao118_1 Tao120_1 Tao121_1
> Tao124_1 Tao126_1 Tao127_1 C001_1 C002_1 C003_1 C004_1 C005_1 C006_1 C007_1
> C008_1 C009_1 C010_1 C011_1 C012_1 C013_1 C014_1 C015_1 C016_1 C017_1
> C018_1 C019_1 C020_1 C021_1 C023_1 C024_1 --hemi lh --meas. area
> --tablefile Area_aseg_stats txt
>
>
>
> File "/usr/local/freesurfer/bin/asegstats2table", line 195
> print 'ERROR: subjects are not specified (use --subjects SUBJECTS)'
>   ^
> SyntaxError: invalid syntax
>
>
>
> I do not know where I am going wrong with this.
>
> Any suggestion would be appreciated.
>
>
>
> Thanks,
>
> Vittal
>
>
>
>
>
>
>
> On Fri, Dec 30, 2022 at 12:33 PM Huang, Yujing 
> wrote:
>
> Hi Vittal,
>
>
>
> I can only repro your error by running ‘python asegstats2table …’.  And
> the alias solution works for me.
>
>
>
> Running ‘asegstats2table’ directly doesn’t give me any errors, and it
> doesn’t need the alias setting.
>
>
>
> Best,
>
>
>
> Yujing
>
>
>
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
> freesurfer-boun...@nmr.mgh.harvard.edu> *On Behalf Of *fsbuild
> *Sent:* Friday, December 30, 2022 12:29 AM
> *To:* freesurfer@nmr.mgh.harvard.edu
> *Cc:* vittalkor...@gmail.com
> *Subject:* Re: [Freesurfer] Help: Aparcstats and asegstats not working
>
>
>
> *External Email - Use Caution*
>
>
> SyntaxError: Missing parentheses in call to 'print'. Did you mean
> print('ERROR: atleast 1 subject must be provided')?
>
> It does not look like you are running a python 2.X.  That may be because
> only python3 is installed by default.
>
>
>
> $ which python
> $ which python2
> $ which python3
> /bin/python3
>
>
>
> … if you need to install python2, you can do it with ...
>
>
>
> $ sudo apt update
>
> $ sudo apt install python2
>
>
>
> $ which python2
>
> /bin/python2
>
> $ python2 --version
> Python 2.7.18
>
>
>
> One way or another you need “python” to report it is a 2.X version *after*
> you set FREESURFER_HOME and source the freesurfer setup script.  To force
> “python” to run as “python2” you can try using an alias,
>
>
>
> $ alias python=python2
>
> $ python --version
> Python 2.7.18
>
> Similarly, if you needed python to run as python3 you could reset the
> alias to use =python3 instead.
>
>
>
> For the error,
>
>  print 'ERROR: subjects are not specified (use --subjects SUBJECTS)’
>
> I would check the subjects you are listing as argument can be found as
> directories under what SUBJECTS_DIR is currently set to.
>
>
>
> - R.
>
>
>
> The information in this e-mail is intended only for the person to whom it
> is addressed.  If you believe this e-

Re: [Freesurfer] Help: Aparcstats and asegstats not working

[Huang, Yujing]

Hi Vittal,

Happy new year!

I’m wondering what the first line is in your 
/usr/local/freesurfer/bin/asegstats2table. Can you check it by doing ‘head 
/usr/local/freesurfer/bin/asegstats2table’ at the prompt?

Can you also try the following?
1. alias python=python2  (as suggested in previous email)
2. python asegstats2table –subjects … --tablefile …

Best,

Yujing



From: vittal korann 
Sent: Friday, December 30, 2022 3:56 PM
To: Huang, Yujing 
Cc: Freesurfer support list 
Subject: Re: [Freesurfer] Help: Aparcstats and asegstats not working


External Email - Use Caution
Thanks, Yujing, for your quick response.

I tried your suggestion as well but the same error keeps appearing.

$ asegstats2table --subjects Met001_1 Met002_1 Met003_1 Met005_1 Met006_1 
Met007_1 Met008_1 Met009_1 Met012_1 Met013_1 Met015_1 Met016_1 Met017_1 
Met018_1 Met019_1 Met020_1 Met021_1 Met022_1 Met023_1 Met024_1 Met025_1 
Met026_1 Met029_1 Met030_1 Met031_1 Met033_1 Met034_1 TOPIRA004_1 TOPIRA005_1 
TOPIRA012_1 TOPIRA013_1 TOPIRA019_1 TOPIRA021_1 TOPIRA022_1 TOPIRA024_1 
TOPIRA025_1 TOPIRA026_1 TOPIRA027_1 TOPIRA029_1 TOPIRA030_1 TOPIRA032_1 
Tao101_1 Tao103_1 Tao104_1 Tao105_1 Tao106_1 Tao107_1 Tao108_1 Tao111_1 
Tao112_1 Tao113_1 Tao115_1 Tao117_1 Tao118_1 Tao120_1 Tao121_1 Tao124_1 
Tao126_1 Tao127_1 C001_1 C002_1 C003_1 C004_1 C005_1 C006_1 C007_1 C008_1 
C009_1 C010_1 C011_1 C012_1 C013_1 C014_1 C015_1 C016_1 C017_1 C018_1 C019_1 
C020_1 C021_1 C023_1 C024_1 --hemi lh --meas. area --tablefile Area_aseg_stats 
txt

File "/usr/local/freesurfer/bin/asegstats2table", line 195
print 'ERROR: subjects are not specified (use --subjects SUBJECTS)'
  ^
SyntaxError: invalid syntax

I do not know where I am going wrong with this.
Any suggestion would be appreciated.

Thanks,
Vittal



On Fri, Dec 30, 2022 at 12:33 PM Huang, Yujing 
mailto:yhuan...@mgh.harvard.edu>> wrote:
Hi Vittal,

I can only repro your error by running ‘python asegstats2table …’.  And the 
alias solution works for me.

Running ‘asegstats2table’ directly doesn’t give me any errors, and it doesn’t 
need the alias setting.

Best,

Yujing

From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 On Behalf Of fsbuild
Sent: Friday, December 30, 2022 12:29 AM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
Cc: vittalkor...@gmail.com<mailto:vittalkor...@gmail.com>
Subject: Re: [Freesurfer] Help: Aparcstats and asegstats not working


External Email - Use Caution

SyntaxError: Missing parentheses in call to 'print'. Did you mean print('ERROR: 
atleast 1 subject must be provided')?
It does not look like you are running a python 2.X.  That may be because only 
python3 is installed by default.

$ which python
$ which python2
$ which python3
/bin/python3

… if you need to install python2, you can do it with ...

$ sudo apt update
$ sudo apt install python2

$ which python2
/bin/python2
$ python2 --version
Python 2.7.18

One way or another you need “python” to report it is a 2.X version *after* you 
set FREESURFER_HOME and source the freesurfer setup script.  To force “python” 
to run as “python2” you can try using an alias,

$ alias python=python2
$ python --version
Python 2.7.18
Similarly, if you needed python to run as python3 you could reset the alias to 
use =python3 instead.

For the error,
 print 'ERROR: subjects are not specified (use --subjects SUBJECTS)’
I would check the subjects you are listing as argument can be found as 
directories under what SUBJECTS_DIR is currently set to.

- R.

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 
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co

Re: [Freesurfer] Help: Aparcstats and asegstats not working

[vittal korann]

External Email - Use Caution

Thanks, Yujing, for your quick response.

I tried your suggestion as well but the same error keeps appearing.

$ asegstats2table --subjects Met001_1 Met002_1 Met003_1 Met005_1 Met006_1
Met007_1 Met008_1 Met009_1 Met012_1 Met013_1 Met015_1 Met016_1 Met017_1
Met018_1 Met019_1 Met020_1 Met021_1 Met022_1 Met023_1 Met024_1 Met025_1
Met026_1 Met029_1 Met030_1 Met031_1 Met033_1 Met034_1 TOPIRA004_1
TOPIRA005_1 TOPIRA012_1 TOPIRA013_1 TOPIRA019_1 TOPIRA021_1 TOPIRA022_1
TOPIRA024_1 TOPIRA025_1 TOPIRA026_1 TOPIRA027_1 TOPIRA029_1 TOPIRA030_1
TOPIRA032_1 Tao101_1 Tao103_1 Tao104_1 Tao105_1 Tao106_1 Tao107_1 Tao108_1
Tao111_1 Tao112_1 Tao113_1 Tao115_1 Tao117_1 Tao118_1 Tao120_1 Tao121_1
Tao124_1 Tao126_1 Tao127_1 C001_1 C002_1 C003_1 C004_1 C005_1 C006_1 C007_1
C008_1 C009_1 C010_1 C011_1 C012_1 C013_1 C014_1 C015_1 C016_1 C017_1
C018_1 C019_1 C020_1 C021_1 C023_1 C024_1 --hemi lh --meas area --tablefile
Area_aseg_stats.txt

File "/usr/local/freesurfer/bin/asegstats2table", line 195
print 'ERROR: subjects are not specified (use --subjects SUBJECTS)'
  ^
SyntaxError: invalid syntax

I do not know where I am going wrong with this.
Any suggestion would be appreciated.

Thanks,
Vittal




On Fri, Dec 30, 2022 at 12:33 PM Huang, Yujing 
wrote:

> Hi Vittal,
>
>
>
> I can only repro your error by running ‘python asegstats2table …’.  And
> the alias solution works for me.
>
>
>
> Running ‘asegstats2table’ directly doesn’t give me any errors, and it
> doesn’t need the alias setting.
>
>
>
> Best,
>
>
>
> Yujing
>
>
>
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
> freesurfer-boun...@nmr.mgh.harvard.edu> *On Behalf Of *fsbuild
> *Sent:* Friday, December 30, 2022 12:29 AM
> *To:* freesurfer@nmr.mgh.harvard.edu
> *Cc:* vittalkor...@gmail.com
> *Subject:* Re: [Freesurfer] Help: Aparcstats and asegstats not working
>
>
>
> *External Email - Use Caution*
>
>
> SyntaxError: Missing parentheses in call to 'print'. Did you mean
> print('ERROR: atleast 1 subject must be provided')?
>
> It does not look like you are running a python 2.X.  That may be because
> only python3 is installed by default.
>
>
>
> $ which python
> $ which python2
> $ which python3
> /bin/python3
>
>
>
> … if you need to install python2, you can do it with ...
>
>
>
> $ sudo apt update
>
> $ sudo apt install python2
>
>
>
> $ which python2
>
> /bin/python2
>
> $ python2 --version
> Python 2.7.18
>
>
>
> One way or another you need “python” to report it is a 2.X version *after*
> you set FREESURFER_HOME and source the freesurfer setup script.  To force
> “python” to run as “python2” you can try using an alias,
>
>
>
> $ alias python=python2
>
> $ python --version
> Python 2.7.18
>
> Similarly, if you needed python to run as python3 you could reset the
> alias to use =python3 instead.
>
>
>
> For the error,
>
>  print 'ERROR: subjects are not specified (use --subjects SUBJECTS)’
>
> I would check the subjects you are listing as argument can be found as
> directories under what SUBJECTS_DIR is currently set to.
>
>
>
> - R.
>
>
>
> 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/19vFAN3khDcvlUskxyhTYI6to-kX38th4pWvDUDnbBWQJ7FR_Ep8Xnq9k97hDZPseTitshpBRLvKMKZEobxZt1MoBl0B_A74appwj9SV8yp995CiBEoy3gKgzdO4GqYX3mRCtT7mPAktjR1Yoe_EAcrqTCFGqKgWzzcWA3tCTAQKZyu7nNnS6ELaWG1BlWXnv9bC8piZd3_myQE9taMNPcDIdlE48cTRZsgSOgyVOMplWZqZ25xi7qIBYE05Q-7DJGaWUzyy69qXcYHJdYpgORxyVKK1UuIXkuYgiMfkRdafxDN-5SMTjA5VLuMnDqxFS/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline
>  .
>
___
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Re: [Freesurfer] Help: Aparcstats and asegstats not working

[vittal korann]

External Email - Use Caution

Thanks, for your quick response.

I installed python2 and did set the default version to python 2.7.18 via
aliasing.
But I am getting the same old errors again. The same terminal responses
were listed below.
The subjects that are used for aseg/aparc are listed in the folder SUBJECTS
under freesurfer

$ asegstats2table --subjects Met001_1 Met002_1 --hemi lh --meas area
--tablefile Area_aseg_stats.txt
 File "/usr/local/freesurfer/bin/aparcstats2table", line 156
print 'ERROR: atleast 1 subject must be provided'
  ^
SyntaxError: Missing parentheses in call to 'print'. Did you mean
print('ERROR: atleast 1 subject must be provided')?

$which python2
/usr/bin/python2

$ python --version
Python 2.7.18

$ export FREESURFER_HOME=/usr/local/freesurfer
$ source $FREESURFER_HOME/SetUpFreeSurfer.sh
 freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c 
Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME   /usr/local/freesurfer
FSFAST_HOME   /usr/local/freesurfer/fsfast
FSF_OUTPUT_FORMAT nii.gz
SUBJECTS_DIR  /usr/local/freesurfer/subjects
MNI_DIR   /usr/local/freesurfer/mni
FSL_DIR   /usr/local/fsl

$ sh aseg_stats_extraction.sh

  File "/usr/local/freesurfer/bin/asegstats2table", line 195
print 'ERROR: subjects are not specified (use --subjects SUBJECTS)'
  ^
SyntaxError: invalid syntax
  File "/usr/local/freesurfer/bin/asegstats2table", line 195
print 'ERROR: subjects are not specified (use --subjects SUBJECTS)'
  ^
SyntaxError: invalid syntax
  File "/usr/local/freesurfer/bin/aparcstats2table", line 156
print 'ERROR: atleast 1 subject must be provided'
  ^
SyntaxError: Missing parentheses in call to 'print'. Did you mean
print('ERROR: atleast 1 subject must be provided')?
  File "/usr/local/freesurfer/bin/aparcstats2table", line 156
print 'ERROR: atleast 1 subject must be provided'
  ^
SyntaxError: Missing parentheses in call to 'print'. Did you mean
print('ERROR: atleast 1 subject must be provided')?

I also attached the shell script file that I created for thickness and area
extraction from the list of subjects.
Is this because something is wrong in the bash_profile/bashrc file? I don't
know I am just guessing.

Any help would be appreciated!

Thanks,
Vittal



On Fri, Dec 30, 2022 at 12:29 AM fsbuild  wrote:

>
> SyntaxError: Missing parentheses in call to 'print'. Did you mean
> print('ERROR: atleast 1 subject must be provided')?
>
> It does not look like you are running a python 2.X.  That may be because
> only python3 is installed by default.
>
> $ which python
> $ which python2
> $ which python3
> /bin/python3
>
> … if you need to install python2, you can do it with ...
>
> $ sudo apt update
> $ sudo apt install python2
>
> $ which python2
> /bin/python2
> $ python2 --version
> Python 2.7.18
>
> One way or another you need “python” to report it is a 2.X version *after*
> you set FREESURFER_HOME and source the freesurfer setup script.  To force
> “python” to run as “python2” you can try using an alias,
>
> $ alias python=python2
> $ python --version
> Python 2.7.18
>
> Similarly, if you needed python to run as python3 you could reset the
> alias to use =python3 instead.
>
> For the error,
>
>  print 'ERROR: subjects are not specified (use --subjects SUBJECTS)’
>
> I would check the subjects you are listing as argument can be found as
> directories under what SUBJECTS_DIR is currently set to.
>
> - R.
>
>
___
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 .
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receiving this message means you understand and accept this risk and wish to 
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Re: [Freesurfer] Help: Aparcstats and asegstats not working

[Huang, Yujing]

Hi Vittal,

I can only repro your error by running ‘python asegstats2table …’.  And the 
alias solution works for me.

Running ‘asegstats2table’ directly doesn’t give me any errors, and it doesn’t 
need the alias setting.

Best,

Yujing

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of fsbuild
Sent: Friday, December 30, 2022 12:29 AM
To: freesurfer@nmr.mgh.harvard.edu
Cc: vittalkor...@gmail.com
Subject: Re: [Freesurfer] Help: Aparcstats and asegstats not working


External Email - Use Caution

SyntaxError: Missing parentheses in call to 'print'. Did you mean print('ERROR: 
atleast 1 subject must be provided')?
It does not look like you are running a python 2.X.  That may be because only 
python3 is installed by default.

$ which python
$ which python2
$ which python3
/bin/python3

… if you need to install python2, you can do it with ...

$ sudo apt update
$ sudo apt install python2

$ which python2
/bin/python2
$ python2 --version
Python 2.7.18

One way or another you need “python” to report it is a 2.X version *after* you 
set FREESURFER_HOME and source the freesurfer setup script.  To force “python” 
to run as “python2” you can try using an alias,

$ alias python=python2
$ python --version
Python 2.7.18
Similarly, if you needed python to run as python3 you could reset the alias to 
use =python3 instead.

For the error,
 print 'ERROR: subjects are not specified (use --subjects SUBJECTS)’
I would check the subjects you are listing as argument can be found as 
directories under what SUBJECTS_DIR is currently set to.

- R.

___
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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 
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Re: [Freesurfer] Help: Aparcstats and asegstats not working

[fsbuild]

External Email - Use Caution

SyntaxError: Missing parentheses in call to 'print'. Did you mean print('ERROR: 
atleast 1 subject must be provided')?It does not look like you are running a 
python 2.X. That may be because only python3 is installed by default.
$ which python
$ which python2
$ which python3
/bin/python3

… if you need to install python2, you can do it with ...
$sudo apt update$ sudo apt install python2
$ which python2/bin/python2$python2 --version
Python 2.7.18

One way or another you need “python” to report it is a 2.X version *after* you 
set FREESURFER_HOME and source the freesurfer setup script. To force 
“python” to run as “python2” you can try using an alias,
$alias python=python2$python --version
Python 2.7.18

Similarly, if you needed python to run as python3 you could reset the alias to 
use =python3 instead.
For the error, 
print 'ERROR: subjects are not specified (use --subjects SUBJECTS)’I 
would check the subjects you are listing as argument can be found as 
directories under what SUBJECTS_DIR is currently set to.
- R.

___
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addressed.  If you believe this e-mail was sent to you in error and the e-mail 
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Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline 
 .
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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] Help: Aparcstats and asegstats not working

[vittal korann]

External Email - Use Caution

Hi Freesurfer experts,

I am trying to collate all morphological parameters like thickness, area,
volume, etc.
When I tried executing the command " asegstats2table --subjects Met001
met002   --hemi lh --meas area --tablefile Area_aseg_stats.txt ", it
failed and I got the below error which is highlighted.

 File "/usr/local/freesurfer/bin/asegstats2table", line 195
print 'ERROR: subjects are not specified (use --subjects SUBJECTS)'
  ^
SyntaxError: invalid syntax
  File "/usr/local/freesurfer/bin/asegstats2table", line 195
print 'ERROR: subjects are not specified (use --subjects SUBJECTS)'
  ^
SyntaxError: invalid syntax
  File "/usr/local/freesurfer/bin/aparcstats2table", line 156
print 'ERROR: atleast 1 subject must be provided'
  ^
SyntaxError: Missing parentheses in call to 'print'. Did you mean
print('ERROR: atleast 1 subject must be provided')?
  File "/usr/local/freesurfer/bin/aparcstats2table", line 156
print 'ERROR: atleast 1 subject must be provided'
  ^
SyntaxError: Missing parentheses in call to 'print'. Did you mean
print('ERROR: atleast 1 subject must be provided')?

I am using the Freesurfer version6 and ubuntu 20.04.
A similar error was reported in the forum and I also tried the suggested
solution by setting python2.7 as the default version. However, nothing has
worked out for me.

Any help would be highly appreaciated.

Thanks,
Vittal
___
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[Freesurfer] HELP! PASSWORD TO UNZIP FS_7_2_0_ubuntu_18_04_06.ova

[Ganeshkaran Mouralidaran]

External Email - Use Caution

Greetings,
I am writing regarding the request to grant the password to
unzip FS_7_2_0_ubuntu_18_04_06.ova file
Thanks and regards,
Ganeshkaran
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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 
 .
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continue communication over unencrypted e-mail, please notify the sender of 
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Re: [Freesurfer] Help: Vertex Properties

[Douglas N. Greve]

The coords are in the surface structure, which you can get by running 
mris_convert lh.white lh.white.asc (asc will be an ascii file)  or by 
loading into matlab with read_surf.m
The surface area is computed for white (?h.area) and pial 
(?h.pial.area). These can be converted to mgz or nifti (mri_convert 
lh.area lh.area.{mgz,nii.gz }) or read into matlab with read_curv.m
The other stuff (angles, edge lengths, dist matrix), you will have to do 
yourself but you can get it on a vertex-wise basis with something like

 mris_info --vx 1000 $SUBJECTS_DIR/fsm011/surf/lh.white
vertexno 1000
xyz  -12.5783 -89.7512 33.0777  # the coords
nxyz -0.9930  0.0542  0.1049  # the normal at this vertex
vertex_area 0.668113   # area
neighbors 6
nbr 0    994 0.6636 0.3354  1524 0.2240
nbr 1    669 0.8749 0.9553  1525 0.3357
nbr 2    677 0.8132 0.6240  1538 0.3472
nbr 3   1006 1.0009 1.0769  2226 0.2301
nbr 4   1408 0.9042 0.8405  2227 0.4085
nbr 5   1419 0.9977 1.0954  2238 0.4587

NbrInfo: nbrno, nbrvno, nbrdist, nbrarea, faceno, facearea

On 11/8/2022 3:43 AM, Sarah Lavelle wrote:


External Email - Use Caution

Hi,

I’m wondering if there’s a way to get the properties of individual 
vertices such as:


1)Coordinates
2)Surface area
3)angles
4) Side lengths
5) distance matrix from other vertices

And can you get these properties for individual surfaces/ 
transformations (eg. On the spherical map or flatmap) ?


On the FreeSurfer application or else through matlab?

Any help would be greatly appreciated,
Thanks,

Sarah

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[Freesurfer] Help: Vertex Properties

[Sarah Lavelle]

External Email - Use Caution

Hi,

I’m wondering if there’s a way to get the properties of individual vertices
such as:

1)Coordinates
2)Surface area
3)angles
4) Side lengths
5) distance matrix from other vertices

And can you get these properties for individual surfaces/ transformations
(eg. On the spherical map or flatmap) ?

On the FreeSurfer application or else through matlab?

Any help would be greatly appreciated,
Thanks,

Sarah
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Re: [Freesurfer] help

[Fischl, Bruce R.,PHD]

Hi Sarah

Sorry, I’m not sure we have much to add. We don’t flatten much any longer, and 
the cuts are kind of ad hoc – the one around the medial wall to get rid of 
non-cortical stuff, then the radial ones from there to remove particularly the 
curvature from the 3 poles. Mostly we just follow what Anders and Marty started 
doing way back when
Bruce

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Sarah Lavelle
Sent: Tuesday, October 25, 2022 5:30 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] help


External Email - Use Caution
Dear freesurfer,

Are there any additional resources on how to make cuts? I have found this 
MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" 
claiming to be 
https://surfer.nmr.mgh.harvard.edu/fswiki/recon-all#Flattening<https://secure-web.cisco.com/18_liDyv7h8S0t-GuSrqbS0mexl0ornQBxqLR6v5JlLJUxICtX_m72JgFOKgqmcmDmNUv_rPvux5Bj3HvJdGS1wmDMB49Af-BJx9Q5hozmhhuUcgnG8xeUpfoO4g2LSz1OdFi_9on9h5ngyGR9FDKKAgMIOCzYJezDsIESZYkKSRdPHkAWMlYTYYAHYx4iD-JqVc30z2DimXPHyrLEyGpNChw8D4PkkLoasWz2jf7w4Pefp9yJvvDnZx-gyl0BhCk8ul3x-2cGVK0SVa-LKxKQHzToFKqsURPjIXBXX2NOr8s_VgCRqHl8WzMW3bCwJiearZFL1Avboe-CZ8CLgZe_w/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2Frecon-all%23Flattening>
 but it isn't enough for the project I am doing. I want to flatten the whole 
surface but I may need to change where I am cutting from patient to patient. 
How do you know how big the hole should be? and how many relaxation cuts should 
you make? How long should they be? If you have any more guidance on how to cut 
to minimise distortion, please let me know!

Also when I perform the mris_flatten function using my patch, my terminal gives 
me a % near the end saying "41% total metric distortion". Can you confirm that 
this value is the total metric distortion from an inflated surface to a flatmap 
surface using my chosen patch?

Many thanks,
Sarah Lavelle
Trinity College Dublin
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[Freesurfer] help

[Sarah Lavelle]

External Email - Use Caution

Dear freesurfer,

Are there any additional resources on how to make cuts? I have found this
https://secure-web.cisco.com/18_liDyv7h8S0t-GuSrqbS0mexl0ornQBxqLR6v5JlLJUxICtX_m72JgFOKgqmcmDmNUv_rPvux5Bj3HvJdGS1wmDMB49Af-BJx9Q5hozmhhuUcgnG8xeUpfoO4g2LSz1OdFi_9on9h5ngyGR9FDKKAgMIOCzYJezDsIESZYkKSRdPHkAWMlYTYYAHYx4iD-JqVc30z2DimXPHyrLEyGpNChw8D4PkkLoasWz2jf7w4Pefp9yJvvDnZx-gyl0BhCk8ul3x-2cGVK0SVa-LKxKQHzToFKqsURPjIXBXX2NOr8s_VgCRqHl8WzMW3bCwJiearZFL1Avboe-CZ8CLgZe_w/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2Frecon-all%23Flattening
 but it isn't
enough for the project I am doing. I want to flatten the whole surface but
I may need to change where I am cutting from patient to patient. How do you
know how big the hole should be? and how many relaxation cuts should you
make? How long should they be? If you have any more guidance on how to cut
to minimise distortion, please let me know!

Also when I perform the mris_flatten function using my patch, my terminal
gives me a % near the end saying "41% total metric distortion". Can you
confirm that this value is the total metric distortion from an inflated
surface to a flatmap surface using my chosen patch?

Many thanks,
Sarah Lavelle
Trinity College Dublin
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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 group analysis

[Douglas N. Greve]

you should be able to generalize two groups/one covariate and/or four 
groups one covariate. don't use gender as a continuous covariate. Make 
sure to normalize your covariates


On 9/26/2022 10:30 AM, fernanda rohrsetzer wrote:


External Email - Use Caution

Hi,
TKS for helping me!
I looked at the examples of the FSGD files, but I believe that my data 
doesn't fit. I've three groups/three factors at three levels (LR=1, 
HR=2, MDD=3) and 6 covariates (gender, age and global brain measure).

I don't know if I was clear in my explanation.


Em seg., 26 de set. de 2022 às 00:06, Douglas N. Greve 
 escreveu:


look at the fsgd examples to see if any fit your situation. Note
that the input needs to be something like
Input    310211    LR 1    15,5    2,678785 645292,6651    152275,2
ie, "LR" instead of "1", etc
using commas (,) instead of points (.) may cause problems

On 9/25/2022 1:10 PM, fernanda rohrsetzer wrote:


External Email - Use Caution

I'm sorry!

attached the FSGD file.

Em dom., 25 de set. de 2022 às 14:10, Douglas N. Greve
 escreveu:

no fsgd file was attached. Also, have you looked at
*MailScanner has detected a possible fraud attempt from
"secure-web.cisco.com" claiming to be*
https://surfer.nmr.mgh.harvard.edu/fswiki/FsgdExamples


?

On 9/23/2022 10:04 AM, fernanda rohrsetzer wrote:


External Email - Use Caution

Hi Freesufer's,
I need to run a group analysis but I don't know how to do
it, the error always appears (print below). There are 3
groups ( risk_group) that I would like to insert as a class
(LR = level 1, HR = level 2 and MDD = level 3) and I would
like to control for sex, age and total brain measure.
Please, if anyone can help me understand what I'm doing
wrong, I'd really appreciate it.
The FSG file is attached
Thank you.


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___
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The information in this e-mail is intended only for the
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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
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<*MailScanner has detected a possible fraud attempt from
"secure-web.cisco.com" claiming to be*

Re: [Freesurfer] Help with group analysis

[fernanda rohrsetzer]

External Email - Use Caution

Hi,
TKS for helping me!
I looked at the examples of the FSGD files, but I believe that my data
doesn't fit. I've three groups/three factors at three levels (LR=1, HR=2,
MDD=3) and 6 covariates (gender, age and global brain measure).
I don't know if I was clear in my explanation.


Em seg., 26 de set. de 2022 às 00:06, Douglas N. Greve <
dgr...@mgh.harvard.edu> escreveu:

> look at the fsgd examples to see if any fit your situation. Note that the
> input needs to be something like
> Input310211LR 115,52,678785645292,6651152275,2
> ie, "LR" instead of "1", etc
> using commas (,) instead of points (.) may cause problems
>
> On 9/25/2022 1:10 PM, fernanda rohrsetzer wrote:
>
> External Email - Use Caution
> I'm sorry!
>
> attached the FSGD file.
>
> Em dom., 25 de set. de 2022 às 14:10, Douglas N. Greve <
> dgr...@mgh.harvard.edu> escreveu:
>
>> no fsgd file was attached. Also, have you looked at *MailScanner has
>> detected a possible fraud attempt from "secure-web.cisco.com" claiming to
>> be* 
>> https://secure-web.cisco.com/1VZjXbFdR2bL-sDVykjA7yRWxHMulxkgtad-yajUBDe5kxieFMAZ3HrhOcJQ4Ylb1ECXqqD14Lr9cjrEixwE2JCoBKSfNEtjioChe3vBXqkfEL-BOCTBrlP4XhJ4OhtlV6lxe1h64ortfnkYeb9ydTazv-Bz0apkHf-geM4IX1QIbECTmFuo-sU9ChDHxeZOr3bavd-NbpqcBSivkroG4ZtVPrx2WFyH2ctoBT2G2QPldZjyfifB1eqJRAi7WuGVlTZrRmIvjoe5zZPwQ8Md6R0-7mmWSDgc0GTtsjqg_FEIYlW7pA1kGgmm3gdxtLHWR1a35UMPhyRJ2tK0Y0Bn4fg/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsgdExamples
>> 
>> ?
>>
>> On 9/23/2022 10:04 AM, fernanda rohrsetzer wrote:
>>
>> External Email - Use Caution
>> Hi Freesufer's,
>> I need to run a group analysis but I don't know how to do it, the error
>> always appears (print below). There are 3 groups ( risk_group) that I would
>> like to insert as a class (LR = level 1, HR = level 2 and MDD = level 3)
>> and I would like to control for sex, age and total brain measure. Please,
>> if anyone can help me understand what I'm doing wrong, I'd really
>> appreciate it.
>> The FSG file is attached
>> Thank you.
>>
>>
>> ___
>> Freesurfer mailing listfreesur...@nmr.mgh.harvard.edu*MailScanner has 
>> detected a possible fraud attempt from "secure-web.cisco.com" claiming to 
>> be* 
>> https://secure-web.cisco.com/1RH_rBab9niiaia8Ck5Hx5E6-yCgZbfEFO7mLl9_xQgPrQQY9dmGd8eTpzDELCl6-z2aQSlhmH4zanLRMiSe-kDfyuGQZsAFkY3obB6Bvb7pa_KPv-TCM7cs3y6a4FIj7TRu4ezFUI9dII028iiGPGgEkIGIQmptIr2JvcSrCy1rCKkV4OG65oJL4Hcvshr-YgzB8ae6WoGhTzszODkoXHbw8s9vrKUoRzgwmbfQ4F-yEBTPvGWt7Rm8aGVq6p19pLRlyjmgNhUCsHg2_WDqadKxIX-Orqk0-z4LRv9wnCbUR2gfiOUgqljyPkhNhBZQng2bWu-f6vYTWuC6itNjMnw/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
>>  
>> 
>>
>>
>> ___
>> 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/1RH_rBab9niiaia8Ck5Hx5E6-yCgZbfEFO7mLl9_xQgPrQQY9dmGd8eTpzDELCl6-z2aQSlhmH4zanLRMiSe-kDfyuGQZsAFkY3obB6Bvb7pa_KPv-TCM7cs3y6a4FIj7TRu4ezFUI9dII028iiGPGgEkIGIQmptIr2JvcSrCy1rCKkV4OG65oJL4Hcvshr-YgzB8ae6WoGhTzszODkoXHbw8s9vrKUoRzgwmbfQ4F-yEBTPvGWt7Rm8aGVq6p19pLRlyjmgNhUCsHg2_WDqadKxIX-Orqk0-z4LRv9wnCbUR2gfiOUgqljyPkhNhBZQng2bWu-f6vYTWuC6itNjMnw/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

Re: [Freesurfer] Help with group analysis

[Douglas N. Greve]

look at the fsgd examples to see if any fit your situation. Note that 
the input needs to be something like

Input    310211    LR 1    15,5    2,678785    645292,6651 152275,2
ie, "LR" instead of "1", etc
using commas (,) instead of points (.) may cause problems

On 9/25/2022 1:10 PM, fernanda rohrsetzer wrote:


External Email - Use Caution

I'm sorry!

attached the FSGD file.

Em dom., 25 de set. de 2022 às 14:10, Douglas N. Greve 
 escreveu:


no fsgd file was attached. Also, have you looked at *MailScanner
has detected a possible fraud attempt from "secure-web.cisco.com"
claiming to be*
https://surfer.nmr.mgh.harvard.edu/fswiki/FsgdExamples


?

On 9/23/2022 10:04 AM, fernanda rohrsetzer wrote:


External Email - Use Caution

Hi Freesufer's,
I need to run a group analysis but I don't know how to do it, the
error always appears (print below). There are 3 groups (
risk_group) that I would like to insert as a class (LR = level 1,
HR = level 2 and MDD = level 3) and I would like to control for
sex, age and total brain measure. Please, if anyone can help me
understand what I'm doing wrong, I'd really appreciate it.
The FSG file is attached
Thank you.


___
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Freesurfer@nmr.mgh.harvard.edu
*MailScanner has detected a possible fraud attempt from
"secure-web.cisco.com" claiming to be*
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer  



___
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*MailScanner has detected a possible fraud attempt from
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>
.


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The information in this e-mail is 

Re: [Freesurfer] Help with group analysis

[fernanda rohrsetzer]

External Email - Use Caution

I'm sorry!

attached the FSGD file.

Em dom., 25 de set. de 2022 às 14:10, Douglas N. Greve <
dgr...@mgh.harvard.edu> escreveu:

> no fsgd file was attached. Also, have you looked at
> https://secure-web.cisco.com/1xDB2MdU7IttZMHh8Wcpy-H4rASI2uqj9-MUHGYt5B5AJhCMmszuKV-viLm47WoU7jm403uKh8mLzeA5xcxQoHZQvsbwcGRWH_ptuX-KXJvDiLaUftl-V1VX6CaHAJNGvDardNN7ga4LKaOP2jpFCH5OG_MBWK71pE00hp5FfRsl5tvuqGeGgetChB4DtXaaEVBwBotJ0slybBFLiZSpKXjmQdl23gdAdN5B0aCJoCDC6yWZKkKkeyzIjf6Ami-wCFlRhMjMz90U_NRs0kpqyZIYvJyQ7a_cWmtIXnsRvMhGLkoGgd9tnwE_xwF_aMu_IkvPfBIn6udwK6L9TVjH0sg/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsgdExamples
>  ?
>
> On 9/23/2022 10:04 AM, fernanda rohrsetzer wrote:
>
> External Email - Use Caution
> Hi Freesufer's,
> I need to run a group analysis but I don't know how to do it, the error
> always appears (print below). There are 3 groups ( risk_group) that I would
> like to insert as a class (LR = level 1, HR = level 2 and MDD = level 3)
> and I would like to control for sex, age and total brain measure. Please,
> if anyone can help me understand what I'm doing wrong, I'd really
> appreciate it.
> The FSG file is attached
> 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://secure-web.cisco.com/1IeS-YL57fzD75MFwwJjA4Sd-7EvX1tlEDghimEHC83PSTZvOaTC6uMGX0MeKlQyTBAimu2DAS98JjAF8rUFAl4eqOG6dAf7DEn9gcnJBQHi7SP8IEjsZrRwbLwfrSOrB4YuKj5JI2j33_LzbO1F75s57wSnEOwgZfit1pTGvtxmDV7iW1wC3FgMxsbk2pZv4Spl1fejTSoTqEdq3IbqUp0br17fLku3me34G20-zVPj6aWecGr4KglnFxOwqfw_g7hoiai7AAwAjveXLBWwL2KQV9IzCL6pLWYPBKbkp_yGV4zQXb15sB4G3WqfLw0smntAbzCh6ZUgoaNxkgrmbiA/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/1lcJ8l8iGsr8svtwqrjcj_YgzO3i4H8osHsQ5MG8o0gSMDmRRUaO02v2siHGL8OJH267EE9rpCJqbHmHeNA2dwDDSYVshI1edCUdw4LQVNdg79MFK7K-hG_m9DSFxk8k4hygrTLezzCgQmakGharcc-FhM6ResORxNNnrX1i0o-P7hJlCk6yBnFeO8G_Om_p-WARUc7EI69ecntT_HF1Pf8o6onpEAWphxwHOeUOjmNjisaQQcB7SwSbhbkp2fZShDqx3TNXAiJUDQyKAaksfscnnb9bpS2-pKhxR1i-NnFejBc0Plkhqxk8X6yb23Fkwd8ftpb22qjX5Eg7_tBHnRg/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline
>  <
> https://secure-web.cisco.com/1lcJ8l8iGsr8svtwqrjcj_YgzO3i4H8osHsQ5MG8o0gSMDmRRUaO02v2siHGL8OJH267EE9rpCJqbHmHeNA2dwDDSYVshI1edCUdw4LQVNdg79MFK7K-hG_m9DSFxk8k4hygrTLezzCgQmakGharcc-FhM6ResORxNNnrX1i0o-P7hJlCk6yBnFeO8G_Om_p-WARUc7EI69ecntT_HF1Pf8o6onpEAWphxwHOeUOjmNjisaQQcB7SwSbhbkp2fZShDqx3TNXAiJUDQyKAaksfscnnb9bpS2-pKhxR1i-NnFejBc0Plkhqxk8X6yb23Fkwd8ftpb22qjX5Eg7_tBHnRg/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline>
>  .
>


w0_group.fsgd 
Description: Binary data
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 .
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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 group analysis

[Douglas N. Greve]

no fsgd file was attached. Also, have you looked at 
https://surfer.nmr.mgh.harvard.edu/fswiki/FsgdExamples ?


On 9/23/2022 10:04 AM, fernanda rohrsetzer wrote:


External Email - Use Caution

Hi Freesufer's,
I need to run a group analysis but I don't know how to do it, the 
error always appears (print below). There are 3 groups ( risk_group) 
that I would like to insert as a class (LR = level 1, HR = level 2 and 
MDD = level 3) and I would like to control for sex, age and total 
brain measure. Please, if anyone can help me understand what I'm doing 
wrong, I'd really appreciate it.

The FSG file is attached
Thank you.


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[Freesurfer] Help with group analysis

[fernanda rohrsetzer]

External Email - Use Caution

Hi Freesufer's,
I need to run a group analysis but I don't know how to do it, the error
always appears (print below). There are 3 groups ( risk_group) that I would
like to insert as a class (LR = level 1, HR = level 2 and MDD = level 3)
and I would like to control for sex, age and total brain measure. Please,
if anyone can help me understand what I'm doing wrong, I'd really
appreciate it.
The FSG file is attached
Thank you.


w0_group.xlsx
Description: MS-Excel 2007 spreadsheet
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Re: [Freesurfer] Help - segmentHA_T1_long.sh "list of time points not found"

[Iglesias Gonzalez, Juan E.,PHD]

Dear Kimi,

When you process the scans longitudinally with FreeSurfer, the file base-tps 
should be created in the subject directory of the template. Isn’t this the case?

Cheers,

/Eugenio

Juan Eugenio Iglesias
http://www.jeiglesias.com





On 19 Sep 2022, at 01:02, Raikkonen Kimi 
mailto:akdaus2...@gmail.com>> wrote:


External Email - Use Caution

Dear FreeSurfer,

Hi, I was trying to run longitudinal analysis of the hippocampus and amygdala 
segmentation pipeline after running the main FreeSurfer longitudinal pipeline.

I ran
segmentHA_T1_long.sh 101_MRI1.long.101_template
segmentHA_T1_long.sh 101_MRI2.long.101_template
segmentHA_T1_long.sh 101_MRI3.long.101_template   etc.

but I got the following error message:
List of time points:
   /study/101_MRI1.long.101_template/base-tps
does not exist




I think I’ve headed the wrong direction, I was wondering how to do the list of 
time points for a subject.
Thanks so much for your help in advance.

Best regards,
Alex
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[Freesurfer] Help - segmentHA_T1_long.sh "list of time points not found"

[Raikkonen Kimi]

External Email - Use Caution

Dear FreeSurfer,

Hi, I was trying to run longitudinal analysis of the hippocampus and amygdala 
segmentation pipeline after running the main FreeSurfer longitudinal pipeline.
 
I ran 
segmentHA_T1_long.sh 101_MRI1.long.101_template
segmentHA_T1_long.sh 101_MRI2.long.101_template
segmentHA_T1_long.sh 101_MRI3.long.101_template   etc.
 
but I got the following error message:
List of time points:
   /study/101_MRI1.long.101_template/base-tps
does not exist
 
 
 
 
I think I’ve headed the wrong direction, I was wondering how to do the list of 
time points for a subject.
Thanks so much for your help in advance.

Best regards,
Alex___
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continue to communicate over unencrypted e-mail. 

[Freesurfer] HELP - pass code for Freesurfer VirtualBox

[Michel Godel]

External Email - Use Caution

Hello,

I am a PhD candidate in neurosciences at the University of Geneva, I would like 
to use Freesurfer on my VirtualBox to benefit from the interface between FS and 
BrainVisa. I write you to ask for the pass code.

Thanks a lot !

Michel

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continue to communicate over unencrypted e-mail. 

[Freesurfer] Help for pass code to open Freesurfer Virtual Machine image (.7z)

[Yuuichi Oosawa]

External Email - Use Caution

Hello,

I'm a student researching Magnetoencephalography estimation and have been
trying to install Freesurfer on a Windows OS using a Virtual Machine,
following the instructions below:

"You will be prompted for a pass code when the archive is successfully
opened. If you do not have the pass code to open the image, then *send an
email to the Freesurfer help list* to receive it."

I do not have the pass code to open it and therefore I'm emailing the
freesurfer help list, please advise.

Thank you for your help in advance!

Yuuichi Oosawa

--
E-Mail: oosawa-yuuichi...@g.ecc.u-tokyo.ac.jp
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[Freesurfer] Help with Pass Code to open Freesurfer on Virtual Machine

[Tatevosyan, Ellen]

External Email - Use Caution

Hello,

I am a neuroimaging researcher and have been trying to install Freesurfer on a 
Windows OS using a Virtual Machine, following the instructions below:

"Download and Run the Virtual Machine:
Ubuntu 18.04.06 compressed image with the Freesurfer 7.2.0 release installed: 
FS_7_2_0_Ubuntu_18_04_06.ova.7z<https://secure-web.cisco.com/1PaZD_uN8-j2duK-8vB8-Bcab_yu4LfPOhhM0EQRGqACIphuTzaQdgiGltX_CURtBCFlEnKO4xEw9ANUNfw9dJl709u6h07OtBMYxPf-5mv7p8Rd8hf65aZqoo_up7BJgP2rWKmGMeDXdkbgdYTzoyoR2f7o0VnpG1GjUzYTPJLV2l5rX5nyAJ2y6gDpaQDfd2wJ3UNZCYT63TNK4sE9dH01LJsJlLq0GA2KPc7jXQ9UupapnyaUmh_SlwVLIxonEKJQj_7nNOiKwywz3Be4fKqUBTsKhiG5AE9Vj53SW-wLCPofRW2pn89wHrsfo3RKUHSamrvAaoUViC00E8-sOaQ/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Fpub%2Fdist%2Ffreesurfer%2F7.2.0%2FFS_7_2_0_ubuntu_18_04_06.ova.7z>

Right click on the .ova.7z file and see what options you have under 
the choices for "Open with". If your current archive program choices cannot 
open a 7zip file, then try installing one of the utilities listed below. You 
will be prompted for a pass code when the archive is successfully opened. If 
you do not have the pass code to open the image, then send an email to the 
Freesurfer help list to receive it."

I do not have the passcode to open the image and therefore am emailing the 
freesurfer help list, please advise.

Best,

Ellen Tatevosyan




UCLA HEALTH SCIENCES IMPORTANT WARNING: This email (and any attachments) is 
only intended for the use of the person or entity to which it is addressed, and 
may contain information that is privileged and confidential. You, the 
recipient, are obligated to maintain it in a safe, secure and confidential 
manner. Unauthorized redisclosure or failure to maintain confidentiality may 
subject you to federal and state penalties. If you are not the intended 
recipient, please immediately notify us by return email, and delete this 
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Re: [Freesurfer] help troubleshooting lta_convert error

[fsbuild]

External Email - Use Caution

Hello Megan,
The errors you list below usually result from running a version of Freesurfer 
that does not match the operating system you are using, i.e., it looks like you 
are trying to run the version built for Ubuntu linux,
7.2.0 (freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b)
… on a CentOS6 system,
Description:  CentOS release 6.7 (Final)
If you have admin privileges on your system, then I would try installing the 
Freesurfer 7.2.0 CentOS6 rpm file on your CentOS6 system, which you can 
download from, 
https://secure-web.cisco.com/1_TrIriXqcfLg6YdYhz-fK97TtRKLaLawhDUmlefqUI_U6mlXmgpjgQk2UXhcwN2NC7TyNy3ieN31qh3FbGtBDSxQ1szMQN7SfmRdFpj7ysB-LpBCtwl5TH7fK4H1H001TDw7DTL2tjz6TTW50f3rwGbs89zFyTAUMfG9E7Gc856Bf8UyftY4htNXC9nvupCoIvaUkjIAeDGtT0Ir_jWBFyzc2ZLLYenGRXDhi1gsEWFCJe7BBe9s42X7KXD71wg5xI_R5f5PnfclBoppYxU9ESHu67HB5DFcg8Fl9ITpQIvU0pANCNzWJSxdGgdm6gY7rbTtZ3b1vG8l46LcvdpnQw/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Fpub%2Fdist%2Ffreesurfer%2F7.2.0%2Ffreesurfer-CentOS6-7.2.0-1.x86_64.rpm
If you do not have admin privs to install the RPM, then you can download and 
expand the tar archive 
from,https://secure-web.cisco.com/1Fhw7EkvdlF04-nFWgMtF44HHWjdGMGEq_-VbJMp12jSu5l2WVbX1_vPjRjQTHB2HY5XwvKzKrLkqZVDPnu_aJXqAcH0GwbhGwRxc1fwpALyZH5Mo4Pc7OpAEk8vQzQOEn6ZdiCjVukVLIoDshJKKcWVg5XB_OBhrYeUXu5OH8cBun2eM_YCigbRGHmwOzS76XnfEX4I3SQKk39JIii0PMjB5zGP0EQEDLtcyOv8Z8WUSPSmsNqls6-NXgCQekj_OMiXrloh2sjr-QTp5XjW_513WvVyJbJ2rjpPE3-9b0A2nGAH4Lk5xK6hxN4JjCM4qAusRy4Kr8BJ-6o8PlsOeHw/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Fpub%2Fdist%2Ffreesurfer%2F7.2.0%2Ffreesurfer-linux-centos6_x86_64-7.2.0.tar.gz
The Freesurfer 7.2.0 distributions available for each operating system are 
currently listed on this 
page,https://secure-web.cisco.com/1Sbf8V045U7e_z5ui8AhyYxoVSIwU0U2mshLiNckTmoysYXiKZ_gXc_vmjX3G-CwmBxGanNK5RoXJ1vwteBU0PTf6LQwTjPCtf6X0MW2rHHcd28Ml4EV6kuZ-8P_24Jy5ppQz4PfGFp1umeUIKtSQAxseIrw50CEtcUQpGMb7HhD1pS7FK0xb_1g-hQbOppeif-4fNt284anghqS_kmzO1fLoNtQh817_Qk4_asTfdz9vXnMhwOK84aO9NQ3tUJsLjUQo3pqVTme4YmmKcO3mX6qBa9Mx0ipQl_oaSL9cKV2N1BKgIncltx7pdb9JhfC2-BcTgPi5dTeLfloC00K0ag/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2Frel7downloads

- R.
On Jul 1, 2022, at 13:32, Megan Schendel mschen...@mrn.org 
wrote:External Email - Use 
CautionHi all,I had a working 
distribution on an old system a few weeks ago, but now I'm getting an 
error. Can anyone offer any troubleshooting ideas?I am working on a 
shared server with a freesurfer distribution that I own.Here is some system 
info:[mschendel@earth scripts]$ lsb_release -aLSB Version:  
:base-4.0-amd64:base-4.0-noarch:core-4.0-amd64:core-4.0-noarch:graphics-4.0-amd64:graphics-4.0-noarch:printing-4.0-amd64:printing-4.0-noarchDistributor
 ID: CentOSDescription:  CentOS release 6.7 (Final)Release:  
  6.7Codename:FinalOn the command line, 
the error looks like this:lta_convert: /lib64/libm.so.6: version `GLIBC_2.27' 
not found (required by lta_convert)lta_convert: /usr/lib64/libstdc++.so.6: 
version `GLIBCXX_3.4.15' not found (required by lta_convert)lta_convert: 
/usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.19' not found (required by 
lta_convert)lta_convert: /lib64/libc.so.6: version `GLIBC_2.14' not found 
(required by lta_convert)The recon-all.log file contains the following:Fri Jul 
1 11:08:24 MDT 2022cd 
/export/research/analysis/unm_psych/dquinn/Navigate_20673/MEG_source_analysis/M87124539setenv
 SUBJECTS_DIR 
/export/research/analysis/unm_psych/dquinn/Navigate_20673/MEG_source_analysis/export/research/analysis/human/jstephen/shared/programs/freesurfer_7.2/freesurfer//bin/recon-all
 -all -i 
/export/research/archive/human/dicom/prisma/dquinn/navigate_20673//M87124539/Study20210623at161830/mprage_5e_32ch_RMS_0003/SerieMR-0003-0001-1.dcm
 -s 
/export/research/analysis/unm_psych/dquinn/Navigate_20673/MEG_source_analysis//M87124539
 -openmp 8subjid M87124539setenv SUBJECTS_DIR 
/export/research/analysis/unm_psych/dquinn/Navigate_20673/MEG_source_analysisFREESURFER_HOME
 
/export/research/analysis/human/jstephen/shared/programs/freesurfer_7.2/freesurfer/Actual
 FREESURFER_HOME 
/export/research/analysis/human/jstephen/shared/programs/freesurfer_7.2/freesurferbuild-stamp.txt:
 
freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76bLinuxearth.mind.unm.edu2.6.32-573.26.1.el6.x86_64
 #1 SMP Wed May 4 00:57:44 UTC 2016 x86_64 x86_64 x86_64 GNU/Linuxcputime 
  unlimitedfilesize   unlimiteddatasize  
 unlimitedstacksize  10240 kbytescoredumpsize 0 
kbytesmemoryuse  unlimitedvmemoryuse  unlimiteddescriptors 
1024memorylocked 64 kbytesmaxproc   
unlimitedprogram versions 
used7.2.0 (freesurfer-linux-ubuntu18_x86_64-7..2.0-20210721-aa8f76b)ERROR: 
Executable 'lta_convert -all-info failed! Is it missing from the 
distribution?'MEG TechnicianPronouns: she/herThe Mind Research Network1101 Yale 
Blvd. NEAlbuquerque, New Mexico 
87106___Freesurfer mailing 

[Freesurfer] help!, I need the pass code to open the FS_7_2_0_Ubuntu_18_04_06.ova.7z

[WenJing]

External Email - Use Caution

Hello FreeSurfer Developers,

I downloaded Vbox from the official website and installed it on my Windows 
system, and then downloaded the FS_7_2_0_Ubuntu_18_04_06.ova.7z, but I need the 
password to successfully open the compressed package, as following picture 
shows, so I sent this email to ask for the password, hoping to get a reply, 
very grateful!___
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[Freesurfer] help troubleshooting lta_convert error

[Megan Schendel]

External Email - Use Caution

Hi all,
I had a working distribution on an old system a few weeks ago, but now I'm
getting an error.  Can anyone offer any troubleshooting ideas?
I am working on a shared server with a freesurfer distribution that I own.

Here is some system info:
[mschendel@earth scripts]$ lsb_release -a
LSB Version:
 
:base-4.0-amd64:base-4.0-noarch:core-4.0-amd64:core-4.0-noarch:graphics-4.0-amd64:graphics-4.0-noarch:printing-4.0-amd64:printing-4.0-noarch
Distributor ID: CentOS
Description:CentOS release 6.7 (Final)
Release:6.7
Codename:   Final

On the command line, the error looks like this:

lta_convert: /lib64/libm.so.6: version `GLIBC_2.27' not found (required by
lta_convert)
lta_convert: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.15' not found
(required by lta_convert)
lta_convert: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.19' not found
(required by lta_convert)
lta_convert: /lib64/libc.so.6: version `GLIBC_2.14' not found (required by
lta_convert)

The recon-all.log file contains the following:

Fri Jul  1 11:08:24 MDT 2022
cd
/export/research/analysis/unm_psych/dquinn/Navigate_20673/MEG_source_analysis/M87124539
setenv SUBJECTS_DIR
/export/research/analysis/unm_psych/dquinn/Navigate_20673/MEG_source_analysis
/export/research/analysis/human/jstephen/shared/programs/freesurfer_7.2/freesurfer//bin/recon-all
-all -i
/export/research/archive/human/dicom/prisma/dquinn/navigate_20673//M87124539/Study20210623at161830/mprage_5e_32ch_RMS_0003/SerieMR-0003-0001-1.dcm
-s
/export/research/analysis/unm_psych/dquinn/Navigate_20673/MEG_source_analysis//M87124539
-openmp 8

subjid M87124539
setenv SUBJECTS_DIR
/export/research/analysis/unm_psych/dquinn/Navigate_20673/MEG_source_analysis
FREESURFER_HOME
/export/research/analysis/human/jstephen/shared/programs/freesurfer_7.2/freesurfer/
Actual FREESURFER_HOME
/export/research/analysis/human/jstephen/shared/programs/freesurfer_7.2/freesurfer
build-stamp.txt: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b
Linux earth.mind.unm.edu 2.6.32-573.26.1.el6.x86_64 #1 SMP Wed May 4
00:57:44 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux
cputime  unlimited
filesize unlimited
datasize unlimited
stacksize10240 kbytes
coredumpsize 0 kbytes
memoryuseunlimited
vmemoryuse   unlimited
descriptors  1024
memorylocked 64 kbytes
maxproc  unlimited



program versions used
7.2.0 (freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b)
ERROR: Executable 'lta_convert -all-info failed! Is it missing from the
distribution?'
MEG Technician
Pronouns: she/her
The Mind Research Network
1101 Yale Blvd. NE
Albuquerque, New Mexico 87106
___
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 .
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Re: [Freesurfer] help - unzip Ubuntu ova password

[fsbuild]

External Email - Use Caution

Sending the info to your email shortly.
- R.On Apr 27, 2022, at 15:31, Dan Lerner d...@findsurgicalsciences.com 
wrote:External Email - Use 
CautionHi,Setting up the Ubuntu 
vm provided by FreeSurfer. I'm emailing for the password as per the 
instructions.Thanks,Dan___Freesurfer
 mailing 
listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer​
___
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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 
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this message immediately.  Continuing to send or respond to e-mail after 
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[Freesurfer] help - unzip Ubuntu ova password

[Dan Lerner]

External Email - Use Caution

Hi,

Setting up the Ubuntu vm provided by FreeSurfer. I'm emailing for the password 
as per the instructions.

Thanks,
Dan
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[Freesurfer] Seeking beta testers for new Freesurfer help forum

[Sennott, Liam Ricker]

Hello, FreeSurfer community,

The FreeSurfer administrative team is working on transitioning the current 
FreeSurfer mailing list infrastructure to a new, more user-friendly platform 
called Discourse. We’re still finalizing the website, so we’re looking for 
potential beta testers for this new platform. As a beta tester, you will post 
your questions to Discourse and interact with the FreeSurfer staff in 
discussion board format.

Please email lsenn...@mgh.harvard.edu if you 
are interested in helping us test this new system!

Thank you,

Liam Sennott
FreeSurfer Admin
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Re: [Freesurfer] Get the password by sending an email request to the freesurfer help list. - Freesurfer VirtualBox Image

[fsbuild]

External Email - Use Caution

Sending the info to your email shortly.
- R.

On Feb 16, 2022, at 10:02, Cristina Pereira Priego 
cristinapereira...@hotmail.com 
wrote:External Email - Use 
CautionHi,My name is Cristina 
and I'm a PhD Student from Clinical Neurosciences Group in IRB LLEIDA. I 
downloaded " Freesurfer VirtualBox Image" and I need the paswword to login as 
the user "developer" in the login menu.I'm waiting for your answer,Best 
regards,Cristina___Freesurfer 
mailing 
listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer​
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[Freesurfer] Get the password by sending an email request to the freesurfer help list. - Freesurfer VirtualBox Image

[Cristina Pereira Priego]

External Email - Use Caution

Hi,

My name is Cristina and I'm a PhD Student from Clinical Neurosciences Group in 
IRB LLEIDA. I downloaded " Freesurfer VirtualBox Image" and I need the paswword 
to login as the user "developer" in the login menu.

I'm waiting for your answer,

Best regards,

Cristina
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Re: [Freesurfer] [Help needed] recon-all log error

[Douglas N. Greve]

you did not point out the lines that worry you. At the end, it says 
"finished without error", which means that you should not visually check 
your results.


On 2/9/2022 6:28 PM, HYE JUNG YOUN wrote:


External Email - Use Caution

Good day,

I hope this email finds you well.

I’d love your assistance with understanding my recon-all.log as I am 
trying to figure out if the reconstruction I’ve done is done properly 
without an error.


But I am seeing a few lines that worries me (please see attached log)

I look forward to hearing from you at your earliest convenience.

Thank you in advance.

Best wishes,

H. Youn

Asan Medical Center

88, Olympic-ro 43-Gil, Songpa-gu, Seoul 05505, Korea


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Re: [Freesurfer] Help

[Douglas N. Greve]

There is an automatic topology fixer in the stream. While sometimes it 
fixes an topo error properly, it does not always do so, so you will need 
to see whether it has fixed is or not. It is the white surface that is 
in error, which is created from the wm.mgz (or filled.mgz), so you will 
need to fix one of those volumes.


On 12/14/2021 5:26 AM, Nilab Nasrullah wrote:


External Email - Use Caution

I am using freesurfer 7.1.This particular subject's segmentation 
didn't include the cerebral cortex of the occipital lobe (see image 
1). Although I can see there are defects in that specific place, there 
are also defects in other places (see atttached images). I have 
followed the instructions on how to correct topological errors but 
that doesn't seem to help much since it is the grey matter that is not 
included in the segmentation.


Can you provide me with some instructions on how to fix these defects?

Thanks,
Nilab

*From:* Douglas N. Greve 
*Sent:* 11 December 2021 00:24
*To:* Nilab Nasrullah ; 
freesurfer@nmr.mgh.harvard.edu 

*Subject:* Re: [Freesurfer] Help
The data look pretty noisy in those images. My guess is that the WM is 
not getting segmented properly in that temporal area or there is an 
incorrectly fixed topology error. Try looking at the wm.mgz (or the 
filled.mgz instead if you have 7.2). YOu can load surface.defects.mgz 
to see where the defects are.


On 11/29/2021 9:41 AM, Nilab Nasrullah wrote:


External Email - Use Caution

Sure. See attached.

//Nilab

*From:* Douglas N. Greve  
<mailto:dgr...@mgh.harvard.edu>

*Sent:* 29 November 2021 15:40
*To:* Nilab Nasrullah  
<mailto:nilab.nasrul...@stud.ki.se>; freesurfer@nmr.mgh.harvard.edu 
<mailto:freesurfer@nmr.mgh.harvard.edu> 
 <mailto:freesurfer@nmr.mgh.harvard.edu>

*Subject:* Re: [Freesurfer] Help
Can you send them in plain, unzipped format?

On 11/29/2021 4:07 AM, Nilab Nasrullah wrote:


External Email - Use Caution

I am attaching a few screenshots of the segmented brain as 
zip-files. Hopefully, you can see the results. If not, let me know 
so I can send it to you in a different format.


Thanks,
Nilab

*From:* freesurfer-boun...@nmr.mgh.harvard.edu 
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> 
 
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Douglas 
N. Greve  <mailto:dgr...@mgh.harvard.edu>

*Sent:* 29 November 2021 04:01
*To:* freesurfer@nmr.mgh.harvard.edu 
<mailto:freesurfer@nmr.mgh.harvard.edu> 
 <mailto:freesurfer@nmr.mgh.harvard.edu>

*Subject:* Re: [Freesurfer] Help
Can you send some pictures?

On 11/23/2021 4:02 AM, Nilab Nasrullah wrote:


External Email - Use Caution

Hi,

I am editing subjects for a research project. After reconstruction, 
some parts of the brain are not included in the segmentation. 
Often, some parts of the temporal lobe and the cortex of the 
occipital lobe are not included. In some cases, the cortex of the 
frontal lobe is also affected.


I have tried using controls points, but the results don't change. I 
have also reconstructed them again, running autorecon1 and 
autorecon2&3 separately. I have lowered the watershed parameters, 
used the gcut command and edited manually after autorecon1 but in 
the end, the results don't vary significantly compared to running 
recon-all -all.


What can I do to include the missing parts?

Thanks,
Nilab



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Re: [Freesurfer] Help

[Douglas N. Greve]

The data look pretty noisy in those images. My guess is that the WM is 
not getting segmented properly in that temporal area or there is an 
incorrectly fixed topology error. Try looking at the wm.mgz (or the 
filled.mgz instead if you have 7.2). YOu can load surface.defects.mgz to 
see where the defects are.


On 11/29/2021 9:41 AM, Nilab Nasrullah wrote:


External Email - Use Caution

Sure. See attached.

//Nilab

*From:* Douglas N. Greve 
*Sent:* 29 November 2021 15:40
*To:* Nilab Nasrullah ; 
freesurfer@nmr.mgh.harvard.edu 

*Subject:* Re: [Freesurfer] Help
Can you send them in plain, unzipped format?

On 11/29/2021 4:07 AM, Nilab Nasrullah wrote:


External Email - Use Caution

I am attaching a few screenshots of the segmented brain as zip-files. 
Hopefully, you can see the results. If not, let me know so I can send 
it to you in a different format.


Thanks,
Nilab

*From:* freesurfer-boun...@nmr.mgh.harvard.edu 
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> 
 
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Douglas 
N. Greve  <mailto:dgr...@mgh.harvard.edu>

*Sent:* 29 November 2021 04:01
*To:* freesurfer@nmr.mgh.harvard.edu 
<mailto:freesurfer@nmr.mgh.harvard.edu> 
 <mailto:freesurfer@nmr.mgh.harvard.edu>

*Subject:* Re: [Freesurfer] Help
Can you send some pictures?

On 11/23/2021 4:02 AM, Nilab Nasrullah wrote:


External Email - Use Caution

Hi,

I am editing subjects for a research project. After reconstruction, 
some parts of the brain are not included in the segmentation. Often, 
some parts of the temporal lobe and the cortex of the occipital lobe 
are not included. In some cases, the cortex of the frontal lobe is 
also affected.


I have tried using controls points, but the results don't change. I 
have also reconstructed them again, running autorecon1 and 
autorecon2&3 separately. I have lowered the watershed parameters, 
used the gcut command and edited manually after autorecon1 but in 
the end, the results don't vary significantly compared to running 
recon-all -all.


What can I do to include the missing parts?

Thanks,
Nilab



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Re: [Freesurfer] Help

[Douglas N. Greve]

Can you send them in plain, unzipped format?

On 11/29/2021 4:07 AM, Nilab Nasrullah wrote:


External Email - Use Caution

I am attaching a few screenshots of the segmented brain as zip-files. 
Hopefully, you can see the results. If not, let me know so I can send 
it to you in a different format.


Thanks,
Nilab

*From:* freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Douglas N. Greve 


*Sent:* 29 November 2021 04:01
*To:* freesurfer@nmr.mgh.harvard.edu 
*Subject:* Re: [Freesurfer] Help
Can you send some pictures?

On 11/23/2021 4:02 AM, Nilab Nasrullah wrote:


External Email - Use Caution

Hi,

I am editing subjects for a research project. After reconstruction, 
some parts of the brain are not included in the segmentation. Often, 
some parts of the temporal lobe and the cortex of the occipital lobe 
are not included. In some cases, the cortex of the frontal lobe is 
also affected.


I have tried using controls points, but the results don't change. I 
have also reconstructed them again, running autorecon1 and 
autorecon2&3 separately. I have lowered the watershed parameters, 
used the gcut command and edited manually after autorecon1 but in the 
end, the results don't vary significantly compared to running 
recon-all -all.


What can I do to include the missing parts?

Thanks,
Nilab



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Re: [Freesurfer] Help

[Douglas N. Greve]

Can you send some pictures?

On 11/23/2021 4:02 AM, Nilab Nasrullah wrote:


External Email - Use Caution

Hi,

I am editing subjects for a research project. After reconstruction, 
some parts of the brain are not included in the segmentation. Often, 
some parts of the temporal lobe and the cortex of the occipital lobe 
are not included. In some cases, the cortex of the frontal lobe is 
also affected.


I have tried using controls points, but the results don't change. I 
have also reconstructed them again, running autorecon1 and 
autorecon2&3 separately. I have lowered the watershed parameters, used 
the gcut command and edited manually after autorecon1 but in the end, 
the results don't vary significantly compared to running recon-all -all.


What can I do to include the missing parts?

Thanks,
Nilab



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att KI kommer att behandla dina personuppgifter. /Här finns 
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.



/Sending email to Karolinska Institutet (KI) will result in KI 
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[Freesurfer] Help

[Nilab Nasrullah]

External Email - Use Caution

Hi,

I am editing subjects for a research project. After reconstruction, some parts 
of the brain are not included in the segmentation. Often, some parts of the 
temporal lobe and the cortex of the occipital lobe are not included. In some 
cases, the cortex of the frontal lobe is also affected.

I have tried using controls points, but the results don't change. I have also 
reconstructed them again, running autorecon1 and autorecon2&3 separately. I 
have lowered the watershed parameters, used the gcut command and edited 
manually after autorecon1 but in the end, the results don't vary significantly 
compared to running recon-all -all.

What can I do to include the missing parts?

Thanks,
Nilab



När du skickar e-post till Karolinska Institutet (KI) innebär detta att KI 
kommer att behandla dina personuppgifter. Här finns information om hur KI 
behandlar 
personuppgifter.


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personal data. You can read more about KI's processing of personal data 
here.
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Re: [Freesurfer] Help

[Fischl, Bruce]

Hi Nilab

Can you send us an example? Usually you can fix this using expert options to 
constrain the range of intensities that white matter is allowed to take

Cheers
Bruce

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Nilab Nasrullah
Sent: Thursday, November 18, 2021 8:01 AM
To: freesurfer@nmr.mgh.harvard.edu
Cc: gr...@nmr.mgh.harvard.edu
Subject: [Freesurfer] Help


External Email - Use Caution
Hi,

I am editing about 120 subjects for a research project. In some 
reconstructions, the grey matter boundary is not recognised, thus Freesurfer 
classifies it as white matter. I have tried to remove additional pial surface 
in the area and it gets a bit better. I have also tried to erase the wm that is 
classified as gm but the results don't change. Using control points is useless 
since the white matter is classified correct. Is there any way I can edit the 
subject to get better boundaries for the grey matter?

Thank you for your help in advance.

//Nilab Nasrullah





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[Freesurfer] Help

[Nilab Nasrullah]

External Email - Use Caution

Hi,

I am editing about 120 subjects for a research project. In some 
reconstructions, the grey matter boundary is not recognised, thus Freesurfer 
classifies it as white matter. I have tried to remove additional pial surface 
in the area and it gets a bit better. I have also tried to erase the wm that is 
classified as gm but the results don't change. Using control points is useless 
since the white matter is classified correct. Is there any way I can edit the 
subject to get better boundaries for the grey matter?

Thank you for your help in advance.

//Nilab Nasrullah



När du skickar e-post till Karolinska Institutet (KI) innebär detta att KI 
kommer att behandla dina personuppgifter. Här finns information om hur KI 
behandlar 
personuppgifter.


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personal data. You can read more about KI's processing of personal data 
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Re: [Freesurfer] Help segmenting all subjects in a folder

[Douglas N. Greve]

That does not apply to the recon-all command, only to 
mri_segment_hypothalamus_subunits



On 7/1/2021 12:23 PM, g.ton...@libero.it wrote:


External Email - Use Caution

Hello FreeSurfer Developers,

Thank you for your work !
I successfully set up Freesurfer and ran a test on my computer, and I 
am now attempting to run recon-all on all subjects in a folder 
("/home/users/s/saccaro/Groupe_0" in the example script below). I run 
the analysis on a HPC (SLURM system).


I found that, concerning the recon-all command, "If no name is given 
after --s, the code will be run on ALL subjects in $SUBJECTS_DIR 
." 
but I do not find information on how this could work also for the 
previous step, mri_convert: is there a way to submit a job to segment 
all subjects in the folder "Groupe_0", and not just S001 (in the 
example below)? All folders are structured as follows: 
/S@@@/scans/struct/@@.nii .


I am new to Freesurfer and I apologize if my question is naive but I 
cannot find a solution in any of the online resources.


Thank you very much for your time!
Best,

Giorgio

*- Script, without SBATCH settings (I join the full version):*

module load FreeSurfer/6.0.0-centos6_x86_64
source /home/users/s/saccaro/SetUpFreeSurfer.sh
FSDIR="/home/users/s/saccaro/Groupe_0"

mksubjdris ${FSDIR}/S001;

mri_convert -i 
${FSDIR}/S001/scans/struct/s44891-153636-1-00192-1.nii -o 
${FSDIR}/S001/scans/struct/s44891-153636-1-00192-1.mgz


recon-all -all -s S001

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[Freesurfer] Help segmenting all subjects in a folder

[g . toniol]

External Email - Use Caution

Hello FreeSurfer Developers,

Thank you for your work ! 
I successfully set up Freesurfer and ran a test on my computer, and I am now 
attempting to run recon-all on all subjects in a folder 
("/home/users/s/saccaro/Groupe_0" in the example script below). I run the 
analysis on a HPC (SLURM system).

I found that, concerning the recon-all command, "If no name is given after --s, 
the code will be run on ALL subjects in $SUBJECTS_DIR 
https://secure-web.cisco.com/1cAYZmFGVfas4DCf91-Y9WZa9anAVybKAgr13rFXfcD8BmuTPUSvDFohmKg6XCOHsIyMh3GxdvII3R4KsnUNvVgmkFYaXaLUrV6D4KS_FHQoG-jh3udJfVenKYjfGnQ52GhpYoVVrX0tBf7dYQrUolGWmFw6e6_WhYzueJZGR4-f7wZgN7ElCR8p-E0JP_iMzorzjxp4ZS3pmsDJZJvZJBPtOe4ViP3yDrkR8Q0-xSgssKu5gO4tvQffgOtxO6IJ39HSHMy99mPGWxaH3WxM5sg/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FHypothalamicSubunits
 ." but I do not find information on how this could work also for the previous 
step, mri_convert: is there a way to submit a job to segment all subjects in 
the folder "Groupe_0", and not just S001 (in the example below)? All folders 
are structured as follows: /S@@@/scans/struct/@@.nii . 

I am new to Freesurfer and I apologize if my question is naive but I cannot 
find a solution in any of the online resources.

Thank you very much for your time!
Best,

Giorgio

- Script, without SBATCH settings (I join the full version):

module load FreeSurfer/6.0.0-centos6_x86_64
source /home/users/s/saccaro/SetUpFreeSurfer.sh
FSDIR="/home/users/s/saccaro/Groupe_0"

mksubjdris ${FSDIR}/S001;

mri_convert -i ${FSDIR}/S001/scans/struct/s44891-153636-1-00192-1.nii -o 
${FSDIR}/S001/scans/struct/s44891-153636-1-00192-1.mgz

recon-all -all -s S001

S001.sh
Description: Bourne shell script
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Re: [Freesurfer] Help with LGI pipeline output - Freeview

[Douglas N. Greve]

First, try using tksurferfv (this is the freeview version of tksurfer; 
tksurfer is obsolete)
Second, you'll have to tell us more than "it did not work" (eg, send the 
terminal output or some other description)


On 6/21/2021 3:03 PM, Lab of Autism and Developmental Neuroscience, Lab 
of Autism and Developmental Neuroscience wrote:


External Email - Use Caution

Dear FreeSurfer experts,

Hope that everyone is well and having a great Monday.

I am having some trouble opening the outputs for the LGI pipeline via 
Freeview - could someone please help me with this?


I tried using + editing the code available on the website *tksurfer 
my_subject_id lh inflated -overlay lh.pial_lgi*; however it did not work.


Thank you so much,
Alex

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[Freesurfer] Help with LGI pipeline output - Freeview

[Lab of Autism and Developmental Neuroscience, Lab of Autism and Developmental Neuroscience]

External Email - Use Caution

Dear FreeSurfer experts,

Hope that everyone is well and having a great Monday.

I am having some trouble opening the outputs for the LGI pipeline via
Freeview - could someone please help me with this?

I tried using + editing the code available on the website *tksurfer
my_subject_id lh inflated -overlay lh.pial_lgi*; however it did not work.

Thank you so much,
Alex
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Re: [Freesurfer] 'help: aparcstats2table'

[Nolan, Jackson]

Hello again,

Thank you for sending the screenshot and additional information.

It looks like your directory structure is correct. It also looks like you are 
correct about the python version causing your error.

That utility is written in Python 2.7, and it appears that your environment is 
sourcing some version of Python 3. (You can confirm this by running the command 
'python --version' in your terminal).

You need to check that you have a version of Python2.7 installed, and then add 
that to your path.

To check that you have a version of Python2.7: run the command 'which python2'. 
If a version of Python2.7 is installed, the path to it will be printed in the 
terminal. If no version of is found, you will need to install one.

To source that python version (add it to your path): run 'export 
PATH="":$PATH'

Best,

Jackson



From: Zeynep Boz 
Sent: Friday, June 4, 2021 2:00 PM
To: Nolan, Jackson 
Subject: Re: 'help: aparcstats2table'


External Email - Use Caution

Dear Jackson,

I run these commands "FreesurferWork on my computer" in the directory 
containing that subject. My subject is H1_deneme in named directory 
FreesurferWork
According to the comments I read, I think this error may be related to the 
phyton version, but of course you know better.
Attached I am sending you a screenshot of the terminal and the folders with the 
file directories.

Thank you for your support
I wish you good work


Dr. Zeynep YÜKSEL
Ondokuz Mayis University
Vocational School of Health Services,
Medical İmaging
55139, Atakum, Samsun, Turkey
Tel: +903623121919 Ext:5261


Kimden: "Nolan, Jackson" 
Kime: "freesurfer" , "zeynep boz" 

Gönderilenler: 2 Haziran Çarşamba 2021 23:20:11
Konu: Re: 'help: aparcstats2table'

Hello Dr. Zeynep,

Are you running those commands in the directory containing that subject? The 
script needs the file path to the subject, and absolute paths tend to work 
better than relative paths.

If you have specified these are still getting those errors, please send your 
full terminal output with the command run and all error messages.

Best,
Jackson

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Zeynep Boz 

Sent: Saturday, May 29, 2021 3:15 PM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: [Freesurfer] 'help: aparcstats2table'


External Email - Use Caution

Hello,
I am using Ubuntu 18.05 version and Freesurfer6 version.
I've completed all the recon-all parts without any problems, but I'm having 
trouble with the "aparcstats2table" part.
The command "aparcstats2table --subject H1_deneme --hemi lh --meas thickness 
--tablefile lh.thicknes.xlsx" gives the following error:
   File "/usr/local/freesurfer/bin/aparcstats2table", line 156
 print 'ERROR: atleast 1 subject must be provided'
   On the command "asegstats2table --subjects H1_deneme H1 --common-segs --meas 
volume --stats = aseg.stats --table = segstats.txt" gives the following error:
   File "/usr/local/freesurfer/bin/asegstats2table", line 195
 print 'ERROR: subjects are not specified (use --subjects SUBJECTS)'
Thank you in advance for your support



Dr.Zeynep YÜKSEL
Ondokuz Mayis University
Vocational School of Health Services,
Medical İmaging
55139, Atakum, Samsun, Turkey
Tel: +903623121919 Ext:5261

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 http://www.massgeneralbrigham.org/complianceline . If 
the e-mail was sent to you in error but does not contain patient information, 
please contact the sender and properly dispose of the e-mail.


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 
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Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-m

Re: [Freesurfer] 'help: aparcstats2table'

[Nolan, Jackson]

Hello Dr. Zeynep,

Are you running those commands in the directory containing that subject? The 
script needs the file path to the subject, and absolute paths tend to work 
better than relative paths.

If you have specified these are still getting those errors, please send your 
full terminal output with the command run and all error messages.

Best,
Jackson

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Zeynep Boz 

Sent: Saturday, May 29, 2021 3:15 PM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: [Freesurfer] 'help: aparcstats2table'


External Email - Use Caution

Hello,
I am using Ubuntu 18.05 version and Freesurfer6 version.
I've completed all the recon-all parts without any problems, but I'm having 
trouble with the "aparcstats2table" part.
The command "aparcstats2table --subject H1_deneme --hemi lh --meas thickness 
--tablefile lh.thicknes.xlsx" gives the following error:
   File "/usr/local/freesurfer/bin/aparcstats2table", line 156
 print 'ERROR: atleast 1 subject must be provided'
   On the command "asegstats2table --subjects H1_deneme H1 --common-segs --meas 
volume --stats = aseg.stats --table = segstats.txt" gives the following error:
   File "/usr/local/freesurfer/bin/asegstats2table", line 195
 print 'ERROR: subjects are not specified (use --subjects SUBJECTS)'
Thank you in advance for your support



Dr.Zeynep YÜKSEL
Ondokuz Mayis University
Vocational School of Health Services,
Medical İmaging
55139, Atakum, Samsun, Turkey
Tel: +903623121919 Ext:5261

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contains patient information, please contact the Mass General Brigham 
Compliance HelpLine at http://www.massgeneralbrigham.org/complianceline . If 
the e-mail was sent to you in error but does not contain patient information, 
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Please note that this e-mail is not secure (encrypted).  If you do not wish to 
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receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail. 

[Freesurfer] 'help: aparcstats2table'

[Zeynep Boz]

External Email - Use Caution

Hello, 
I am using Ubuntu 18.05 version and Freesurfer6 version. 
I've completed all the recon-all parts without any problems, but I'm having 
trouble with the "aparcstats2table" part. 
The command "aparcstats2table --subject H1_deneme --hemi lh --meas thickness 
--tablefile lh.thicknes.xlsx" gives the following error: 
File "/usr/local/freesurfer/bin/aparcstats2table", line 156 
print 'ERROR: atleast 1 subject must be provided' 
On the command "asegstats2table --subjects H1_deneme H1 --common-segs --meas 
volume --stats = aseg.stats --table = segstats.txt" gives the following error: 
File "/usr/local/freesurfer/bin/asegstats2table", line 195 
print 'ERROR: subjects are not specified (use --subjects SUBJECTS)' 
Thank you in advance for your support 



Dr.Zeynep YÜKSEL 
Ondokuz Mayis University 
Vocational School of Health Services, 
Medical İmaging 
55139, Atakum, Samsun, Turkey 
Tel: +903623121919 Ext:5261 

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Re: [Freesurfer] help Optseq2 study design

[Douglas N. Greve]

On 5/17/2021 10:16 AM, Ellen JOOS wrote:

External Email - Use Caution
Dear Freesurfer team,

I am currently preparing my first fMRI study and used OptSeq2 for 
creating the trial sequence. Since I am not experienced with the study 
design in MRI (I mainly conducted EEG studies so far), I would like to 
have your professional opinion on my design choices and use of your 
program.


The parameters of my study are the following:

I will conduct a multiband fMRI study with an event-related design 
that will have a TR of 0.5s. I will present 10 different types of 
trials that will have a length of 2.5s each, but that will be shown 
with different amounts of repetitions across the experiment. Within 
the 2.5s trial time, I included a fixed time period of 1.3s to respond.


As indicated in your recommendations, I added time to the overall 
presentation time for the "NULL events" that corresponds to the time 
needed for one of my trial types (as if I would have another trial 
type). You can find the output of OptSeq attached.


My questions are the following:

1) Did I use the program correctly by having a fixed response time 
window within the trial duration estimation?

Yes


2) Is the use of the NULL events (as can be seen in the attached file) 
correct and sufficient to introduce varying amounts of time between 
the individual trials such that the hemodynamic response can be 
captured appropriately?
This is a tricky question because you end up not having many nulls 
relative to your task, so they might look a little like odd balls (eg, 
at one point there are 7 task trials between nulls). This is more of a 
question for you and whether you think the psychology is affected by the 
nulls. I would probably double the null time.


3) In the summary of the OptSeq results, I found an efficiency value 
of 0.009 and a VRFAvg of 6.24. I saw in your recommendations that the 
VRFAvg should be 20-40. Is the result of my calcuation too bad to have 
an efficient recording that allows analyzing the data in an 
event-related manner?
Are you planning to use an FIR or are you going to assume a shape to the 
HRF? Probably the latter; if so, then those values are not meaningful.


4) In the actual experiment I will present the attached sequence 
twice. I have now the options to either present two different 
sequences (e.g. the two most efficient sequences produced by OptSeq) 
or to repeat the most efficient sequence twice. Do you have a 
recommendation? And further, might using the same sequence across 
participants result in a general ordering effect that might bias my 
results?
I would use two different sequences and then randomize the order across 
subjects.



I am very much looking forward to your response and already thank you 
for your advice and help!


Kind regards,

Ellen Joos


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[Freesurfer] help Optseq2 study design

[Ellen JOOS]

   External Email - Use Caution


Dear Freesurfer team,

I am currently preparing my first fMRI study and used OptSeq2 for 
creating the trial sequence. Since I am not experienced with the study 
design in MRI (I mainly conducted EEG studies so far), I would like to 
have your professional opinion on my design choices and use of your program.


The parameters of my study are the following:

I will conduct a multiband fMRI study with an event-related design that 
will have a TR of 0.5s. I will present 10 different types of trials that 
will have a length of 2.5s each, but that will be shown with different 
amounts of repetitions across the experiment. Within the 2.5s trial 
time, I included a fixed time period of 1.3s to respond.


As indicated in your recommendations, I added time to the overall 
presentation time for the "NULL events" that corresponds to the time 
needed for one of my trial types (as if I would have another trial 
type). You can find the output of OptSeq attached.


My questions are the following:

1) Did I use the program correctly by having a fixed response time 
window within the trial duration estimation?


2) Is the use of the NULL events (as can be seen in the attached file) 
correct and sufficient to introduce varying amounts of time between the 
individual trials such that the hemodynamic response can be captured 
appropriately?


3) In the summary of the OptSeq results, I found an efficiency value of 
0.009 and a VRFAvg of 6.24. I saw in your recommendations that the 
VRFAvg should be 20-40. Is the result of my calcuation too bad to have 
an efficient recording that allows analyzing the data in an 
event-related manner?


4) In the actual experiment I will present the attached sequence twice. 
I have now the options to either present two different sequences (e.g. 
the two most efficient sequences produced by OptSeq) or to repeat the 
most efficient sequence twice. Do you have a recommendation? And 
further, might using the same sequence across participants result in a 
general ordering effect that might bias my results?



I am very much looking forward to your response and already thank you 
for your advice and help!


Kind regards,

Ellen Joos

--
Dr. rer. nat. Ellen JOOS

INSERM U1114
Hôpital Civil / Clinique psychiatrique
1 place de l'hôpital
67085 STRASBOURG

Tel: +33.3.88.11.61.31



optseq_MRI_CondSL.ods
Description: application/vnd.oasis.opendocument.spreadsheet
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Re: [Freesurfer] help with SAMSEG

[Hoopes, Andrew]

The atlases used by samseg are very different from freesurfer GCAs, and the 
samseg-template creation is not an easily-accessible utility at the moment. 
Feel free to look through the GEMS code in the FS repository, but it might be 
some time before we have an easy-to-use samseg atlas building tool in 
freesurfer.

Best
Andrew

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Alberto Del Cerro Leon 

Date: Wednesday, May 5, 2021 at 11:11 AM
To: Freesurfer support list 
Subject: [Freesurfer] help with SAMSEG

External Email - Use Caution
Hello Freesurfer team, my group is interested in using the SAMSEG tool to 
evaluate white matter lesions in MCI patients. We would like to use a 
personalized atlas for the measure. We suppose that we need to use the flag 
--atlas but we don`t know if we need a generic atlas or we need an atlas at 
each subject' spaces.

Thanks in advance for your help.
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[Freesurfer] help with SAMSEG

[Alberto Del Cerro Leon]

External Email - Use Caution

Hello Freesurfer team, my group is interested in using the SAMSEG tool to
evaluate white matter lesions in MCI patients. We would like to use a
personalized atlas for the measure. We suppose that we need to use the flag
--atlas but we don`t know if we need a generic atlas or we need an atlas at
each subject' spaces.

Thanks in advance for your help.
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Re: [Freesurfer] Help

[Douglas N. Greve]

We don't have a lobar segmentation. You can get whole cerebellum (GM and 
WM) from our standard analysis (recon-all) or using samseg.

On 3/5/2021 3:27 PM, Murray Howerth wrote:
>  External Email - Use Caution
>
> I am new to this platform and would like some direction as how to obtain 
> adjusted cerebellar volumes, specifically lobular cerebellum structure.
> With thanks,
> M
>
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[Freesurfer] Help

[Murray Howerth]

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I am new to this platform and would like some direction as how to obtain 
adjusted cerebellar volumes, specifically lobular cerebellum structure.
With thanks, 
M

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Re: [Freesurfer] help with labels

[Douglas N. Greve]

You can manully edit the annotation or you can manually edit the AAL 
segmentation to fill in the holes


On 1/28/2021 6:09 AM, Alberto Del Cerro Leon wrote:


External Email - Use Caution

I found the vertex for the holes but how can i modify them or how can 
I solve them?


El mié, 27 ene 2021 a las 16:36, Douglas N. Greve 
(mailto:dgr...@mgh.harvard.edu>>) escribió:


Look at the surface superimposed on the volume along with the AAL
segmentation to make sure that it intersects the segmentation at
all vertices. You can find the vertex numbers for the holes, and
then go specifically to that vertex

On 1/27/2021 6:27 AM, Alberto Del Cerro Leon wrote:


External Email - Use Caution

Hello Freesurfer team, I did an AAL atlas on the surface using
mri_vol2surf, however when I look at this overlay there are many
holes in the labels with vertices that don't belong to any label.
Could u help me with this problem?

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Re: [Freesurfer] help with labels

[Alberto Del Cerro Leon]

External Email - Use Caution

I found the vertex for the holes but how can i modify them or how can I
solve them?

El mié, 27 ene 2021 a las 16:36, Douglas N. Greve ()
escribió:

> Look at the surface superimposed on the volume along with the AAL
> segmentation to make sure that it intersects the segmentation at all
> vertices. You can find the vertex numbers for the holes, and then go
> specifically to that vertex
>
> On 1/27/2021 6:27 AM, Alberto Del Cerro Leon wrote:
>
> External Email - Use Caution
> Hello Freesurfer team, I did an AAL atlas on the surface using
> mri_vol2surf, however when I look at this overlay there are many holes in
> the labels with vertices that don't belong to any label. Could u help me
> with this problem?
>
> ___
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>
>
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Re: [Freesurfer] help with labels

[Douglas N. Greve]

Look at the surface superimposed on the volume along with the AAL 
segmentation to make sure that it intersects the segmentation at all 
vertices. You can find the vertex numbers for the holes, and then go 
specifically to that vertex


On 1/27/2021 6:27 AM, Alberto Del Cerro Leon wrote:


External Email - Use Caution

Hello Freesurfer team, I did an AAL atlas on the surface using 
mri_vol2surf, however when I look at this overlay there are many holes 
in the labels with vertices that don't belong to any label. Could u 
help me with this problem?


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[Freesurfer] help with labels

[Alberto Del Cerro Leon]

External Email - Use Caution

Hello Freesurfer team, I did an AAL atlas on the surface using
mri_vol2surf, however when I look at this overlay there are many holes in
the labels with vertices that don't belong to any label. Could u help me
with this problem?
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Re: [Freesurfer] Help with mergecontrasts-sess function

[Douglas N. Greve]

They way you have specified your contrast is a conjunction of individual 
contrasts, ie, cA>cAc AND cB>cBc. If that what you want? Originally, you 
were just asking about  the interaction

On 1/26/2021 5:17 AM, Paula Maldonado wrote:
>  External Email - Use Caution
>
> Thanks for your reply,
> However I have now a doubt regarding one aspect that I had not noticed before.
>
> What I wanted to do is to perform the contrast 
> (condA>condAcontrol)>(condB>condBcontrol) with the order of my condition 
> being condA, condAcontrol, condB, condBcontrol
>
> You said that to do so I should use -a 1 -c 2 -c 3 -a 4, but I don’t 
> understand why condition 3 is -c and condition 4 is -a.
> To my understanding a is assigning a positive weight to my predictors, while 
> c is assigning a negative one.
> So if I run  -a 1 -c 2 -c 3 -a 4, am I not testing the contrast 
> (condA>condAcontrol)>(condBcontrol>condB) ?
>
> In addition, if now I want to obtain: 
> (condA>condB)>(condAcontrol>condBcontrol)
> should I run mkcontrast-sess -analysis analysis -contrast contrastname -a 1 
> -c 3 -c 2 -a 4, or -a 1 -c 3 -a 2 -c 4?
>
>
> Thanks,
>
>
> Paula
>
>
>> Il giorno 27 ott 2020, alle ore 22:50, Douglas N. Greve 
>>  ha scritto:
>>
>> You would just run mkcontrast-sess, eg, if your four conditions are
>> ordered condA, condAcontrol, condB, condBcont, then
>> mkcontrast-sess -analysis analysis -contrast contrastname -a 1 -c 2 -c 3
>> -a 4
>> If you want it reversed, then just reverse the a's and c's
>>
>> On 10/23/2020 4:39 AM, Paula Maldonado wrote:
>>>  External Email - Use Caution
>>>
>>> Dear experts,
>>> I am running an fMRI experiment in which I have four conditions: two main 
>>> conditions (condition A and condition B) and two respective control 
>>> conditions (condition Acontrol and condition Bcontrol).
>>> I would like to create a map showing significantly greater activity for 
>>> condition A relative to condition B, after subtracting out the activity for 
>>> the respective control conditions. In other words, I would like to perform 
>>> the following contrast:
>>> (condition A - condition A control) - (condition B - condition B control)
>>> Then I would like to have a map that shows the reverse contrast 
>>> too:(condition B - condition B control) - (condition A - condition A 
>>> control).
>>>
>>> How do I do that?To obtain the first map: (condition A - condition A 
>>> control) - (condition B - condition B control) I have tried with the 
>>> mergecontrasts-sess function with the -conjunction flag and the OR option 
>>> as detailed below:
>>> mergecontrasts-sess -mergedcontrast conjres -conjunction or -analysis 
>>> analysisname -map sig -space sph -isxavg fixed -contrast Contrast1 2 pos 0 
>>> -contrast Contrast 2 pos 0 -s sessionsfMRI/Sub01/bold -hemi lh
>>>
>>> where Contrast1= (condition A - condition A control) and Contrast2= 
>>> (condition B - condition B control)
>>> however the map I get is exactly the same as (condition A - condition A 
>>> control), as if subtracting out Contrast 2 had no impact on the map.
>>>
>>> Thanks,
>>>
>>> Paula
>>>
>>>
>>>
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Re: [Freesurfer] Help with mergecontrasts-sess function

[Paula Maldonado]

External Email - Use Caution

Thanks for your reply, 
However I have now a doubt regarding one aspect that I had not noticed before.

What I wanted to do is to perform the contrast 
(condA>condAcontrol)>(condB>condBcontrol) with the order of my condition being 
condA, condAcontrol, condB, condBcontrol

You said that to do so I should use -a 1 -c 2 -c 3 -a 4, but I don’t understand 
why condition 3 is -c and condition 4 is -a.
To my understanding a is assigning a positive weight to my predictors, while c 
is assigning a negative one.
So if I run  -a 1 -c 2 -c 3 -a 4, am I not testing the contrast 
(condA>condAcontrol)>(condBcontrol>condB) ?

In addition, if now I want to obtain: (condA>condB)>(condAcontrol>condBcontrol) 
should I run mkcontrast-sess -analysis analysis -contrast contrastname -a 1 -c 
3 -c 2 -a 4, or -a 1 -c 3 -a 2 -c 4?


Thanks, 


Paula


> Il giorno 27 ott 2020, alle ore 22:50, Douglas N. Greve 
>  ha scritto:
> 
> You would just run mkcontrast-sess, eg, if your four conditions are 
> ordered condA, condAcontrol, condB, condBcont, then
> mkcontrast-sess -analysis analysis -contrast contrastname -a 1 -c 2 -c 3 
> -a 4
> If you want it reversed, then just reverse the a's and c's
> 
> On 10/23/2020 4:39 AM, Paula Maldonado wrote:
>> External Email - Use Caution
>> 
>> Dear experts,
>> I am running an fMRI experiment in which I have four conditions: two main 
>> conditions (condition A and condition B) and two respective control 
>> conditions (condition Acontrol and condition Bcontrol).
>> I would like to create a map showing significantly greater activity for 
>> condition A relative to condition B, after subtracting out the activity for 
>> the respective control conditions. In other words, I would like to perform 
>> the following contrast:
>> (condition A - condition A control) - (condition B - condition B control)
>> Then I would like to have a map that shows the reverse contrast 
>> too:(condition B - condition B control) - (condition A - condition A 
>> control).
>> 
>> How do I do that?To obtain the first map: (condition A - condition A 
>> control) - (condition B - condition B control) I have tried with the 
>> mergecontrasts-sess function with the -conjunction flag and the OR option as 
>> detailed below:
>> mergecontrasts-sess -mergedcontrast conjres -conjunction or -analysis 
>> analysisname -map sig -space sph -isxavg fixed -contrast Contrast1 2 pos 0 
>> -contrast Contrast 2 pos 0 -s sessionsfMRI/Sub01/bold -hemi lh
>> 
>> where Contrast1= (condition A - condition A control) and Contrast2= 
>> (condition B - condition B control)
>> however the map I get is exactly the same as (condition A - condition A 
>> control), as if subtracting out Contrast 2 had no impact on the map.
>> 
>> Thanks,
>> 
>> Paula
>> 
>> 
>> 
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Re: [Freesurfer] Help with mergecontrasts-sess function {Disarmed}

[Greve, Douglas N.,Ph.D.]

If you want a cluster table, then you will have to run mri_surfcluster on the 
output of the conjunction. Run it with --help and write back if you need more 
info

On 11/21/2020 10:03 AM, Paula Maldonado wrote:

External Email - Use Caution

Dear Douglas,

Could you please tell me where can I find the cluster table?

Thank you,
Best regards,

Paula

Il giorno 11 nov 2020, alle ore 17:32, Douglas N. Greve 
mailto:dgr...@mgh.harvard.edu>> ha scritto:

There is not a summary table, it is just a map. Do you want a cluster table?

On 11/10/2020 11:26 AM, Paula Maldonado wrote:

External Email - Use Caution

Thanks for your reply, that worked. Can you please tell me where I can find a 
summary table of the activated regions resulting from the conjunction analysis?

Best regards,

Paula




Il giorno 27 ott 2020, alle ore 22:50, Douglas N. Greve 
mailto:dgr...@mgh.harvard.edu>> ha scritto:

You would just run mkcontrast-sess, eg, if your four conditions are
ordered condA, condAcontrol, condB, condBcont, then
mkcontrast-sess -analysis analysis -contrast contrastname -a 1 -c 2 -c 3
-a 4
If you want it reversed, then just reverse the a's and c's

On 10/23/2020 4:39 AM, Paula Maldonado wrote:
External Email - Use Caution

Dear experts,
I am running an fMRI experiment in which I have four conditions: two main 
conditions (condition A and condition B) and two respective control conditions 
(condition Acontrol and condition Bcontrol).
I would like to create a map showing significantly greater activity for 
condition A relative to condition B, after subtracting out the activity for the 
respective control conditions. In other words, I would like to perform the 
following contrast:
(condition A - condition A control) - (condition B - condition B control)
Then I would like to have a map that shows the reverse contrast too:(condition 
B - condition B control) - (condition A - condition A control).

How do I do that?To obtain the first map: (condition A - condition A control) - 
(condition B - condition B control) I have tried with the mergecontrasts-sess 
function with the -conjunction flag and the OR option as detailed below:
mergecontrasts-sess -mergedcontrast conjres -conjunction or -analysis 
analysisname -map sig -space sph -isxavg fixed -contrast Contrast1 2 pos 0 
-contrast Contrast 2 pos 0 -s sessionsfMRI/Sub01/bold -hemi lh

where Contrast1= (condition A - condition A control) and Contrast2= (condition 
B - condition B control)
however the map I get is exactly the same as (condition A - condition A 
control), as if subtracting out Contrast 2 had no impact on the map.

Thanks,

Paula



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Re: [Freesurfer] Help with mergecontrasts-sess function {Disarmed}

[Paula Maldonado]

External Email - Use Caution

Dear Douglas, 

Could you please tell me where can I find the cluster table?

Thank you, 
Best regards, 

Paula

> Il giorno 11 nov 2020, alle ore 17:32, Douglas N. Greve 
>  ha scritto:
> 
> There is not a summary table, it is just a map. Do you want a cluster table?
> 
> On 11/10/2020 11:26 AM, Paula Maldonado wrote:
>> External Email - Use Caution
>> 
>> Thanks for your reply, that worked. Can you please tell me where I can find 
>> a summary table of the activated regions resulting from the conjunction 
>> analysis?
>> 
>> Best regards,
>> 
>> Paula
>> 
>> 
>> 
>> 
>>> Il giorno 27 ott 2020, alle ore 22:50, Douglas N. Greve 
>>> mailto:dgr...@mgh.harvard.edu>> ha scritto:
>>> 
>>> You would just run mkcontrast-sess, eg, if your four conditions are 
>>> ordered condA, condAcontrol, condB, condBcont, then
>>> mkcontrast-sess -analysis analysis -contrast contrastname -a 1 -c 2 -c 3 
>>> -a 4
>>> If you want it reversed, then just reverse the a's and c's
>>> 
>>> On 10/23/2020 4:39 AM, Paula Maldonado wrote:
 External Email - Use Caution
 
 Dear experts,
 I am running an fMRI experiment in which I have four conditions: two main 
 conditions (condition A and condition B) and two respective control 
 conditions (condition Acontrol and condition Bcontrol).
 I would like to create a map showing significantly greater activity for 
 condition A relative to condition B, after subtracting out the activity 
 for the respective control conditions. In other words, I would like to 
 perform the following contrast:
 (condition A - condition A control) - (condition B - condition B control)
 Then I would like to have a map that shows the reverse contrast 
 too:(condition B - condition B control) - (condition A - condition A 
 control).
 
 How do I do that?To obtain the first map: (condition A - condition A 
 control) - (condition B - condition B control) I have tried with the 
 mergecontrasts-sess function with the -conjunction flag and the OR option 
 as detailed below:
 mergecontrasts-sess -mergedcontrast conjres -conjunction or -analysis 
 analysisname -map sig -space sph -isxavg fixed -contrast Contrast1 2 pos 0 
 -contrast Contrast 2 pos 0 -s sessionsfMRI/Sub01/bold -hemi lh
 
 where Contrast1= (condition A - condition A control) and Contrast2= 
 (condition B - condition B control)
 however the map I get is exactly the same as (condition A - condition A 
 control), as if subtracting out Contrast 2 had no impact on the map.
 
 Thanks,
 
 Paula
 
 
 
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Re: [Freesurfer] Help with MRI labels {Disarmed}

[Alberto Del Cerro Leon]

External Email - Use Caution

I want to obtain gray matter, withe matter volume, thickness and curvature
based on AAL segmentation.

El jue., 12 nov. 2020 15:27, Douglas N. Greve 
escribió:

> So you want the AAL atlas on the surface? If so, then run recon-all on the
> AAL anatomical T1w volume template, then use mri_vol2surf to sample the
> labels on the surface, then use this surface segmentation or extract labels
> (mri_cor2label with --surf option) or convert to an annotation
> (mris_seg2annot)
>
>
> On 11/11/2020 11:32 AM, Alberto Del Cerro Leon wrote:
>
> External Email - Use Caution
> Good afternoon, my name is Alberto del Cerro and I am a PhD student in the
> cognitive and computational neuroscience laboratory (LNCyC) at the
> biomedical technology center (CTB) of the Polytechnic University of Madrid
> (UPM). I am currently extracting the structural data from the T1 images of
> my project and I would like to extract the volume, thickness and curvature
> data in the regions of interest where I obtained results in
> electrophysiology (MEG). The point is that for this data I used the AAL
> atlas and I would like to use these regions to obtain structural data in
> FreeSurfer. Researching on the internet I have read that this is possible
> with the mri_label2vol command but I would like to know how I can proceed
> to obtain this data. Can you guide me in this process?
>
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>
>
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Re: [Freesurfer] Help with MRI labels

[Douglas N. Greve]

So you want the AAL atlas on the surface? If so, then run recon-all on 
the AAL anatomical T1w volume template, then use mri_vol2surf to sample 
the labels on the surface, then use this surface segmentation or extract 
labels (mri_cor2label with --surf option) or convert to an annotation 
(mris_seg2annot)



On 11/11/2020 11:32 AM, Alberto Del Cerro Leon wrote:


External Email - Use Caution

Good afternoon, my name is Alberto del Cerro and I am a PhD student in 
the cognitive and computational neuroscience laboratory (LNCyC) at the 
biomedical technology center (CTB) of the Polytechnic University of 
Madrid (UPM). I am currently extracting the structural data from the 
T1 images of my project and I would like to extract the volume, 
thickness and curvature data in the regions of interest where I 
obtained results in electrophysiology (MEG). The point is that for 
this data I used the AAL atlas and I would like to use these regions 
to obtain structural data in FreeSurfer. Researching on the internet I 
have read that this is possible with the mri_label2vol command but I 
would like to know how I can proceed to obtain this data. Can you 
guide me in this process?


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Re: [Freesurfer] Help with mergecontrasts-sess function {Disarmed}

[Paula Maldonado]

External Email - Use Caution

Yes, please,

Best regards, 

Paula

> Il giorno 11 nov 2020, alle ore 17:32, Douglas N. Greve 
>  ha scritto:
> 
> There is not a summary table, it is just a map. Do you want a cluster table?
> 
> On 11/10/2020 11:26 AM, Paula Maldonado wrote:
>> External Email - Use Caution
>> 
>> Thanks for your reply, that worked. Can you please tell me where I can find 
>> a summary table of the activated regions resulting from the conjunction 
>> analysis?
>> 
>> Best regards,
>> 
>> Paula
>> 
>> 
>> 
>> 
>>> Il giorno 27 ott 2020, alle ore 22:50, Douglas N. Greve 
>>> mailto:dgr...@mgh.harvard.edu>> ha scritto:
>>> 
>>> You would just run mkcontrast-sess, eg, if your four conditions are 
>>> ordered condA, condAcontrol, condB, condBcont, then
>>> mkcontrast-sess -analysis analysis -contrast contrastname -a 1 -c 2 -c 3 
>>> -a 4
>>> If you want it reversed, then just reverse the a's and c's
>>> 
>>> On 10/23/2020 4:39 AM, Paula Maldonado wrote:
 External Email - Use Caution
 
 Dear experts,
 I am running an fMRI experiment in which I have four conditions: two main 
 conditions (condition A and condition B) and two respective control 
 conditions (condition Acontrol and condition Bcontrol).
 I would like to create a map showing significantly greater activity for 
 condition A relative to condition B, after subtracting out the activity 
 for the respective control conditions. In other words, I would like to 
 perform the following contrast:
 (condition A - condition A control) - (condition B - condition B control)
 Then I would like to have a map that shows the reverse contrast 
 too:(condition B - condition B control) - (condition A - condition A 
 control).
 
 How do I do that?To obtain the first map: (condition A - condition A 
 control) - (condition B - condition B control) I have tried with the 
 mergecontrasts-sess function with the -conjunction flag and the OR option 
 as detailed below:
 mergecontrasts-sess -mergedcontrast conjres -conjunction or -analysis 
 analysisname -map sig -space sph -isxavg fixed -contrast Contrast1 2 pos 0 
 -contrast Contrast 2 pos 0 -s sessionsfMRI/Sub01/bold -hemi lh
 
 where Contrast1= (condition A - condition A control) and Contrast2= 
 (condition B - condition B control)
 however the map I get is exactly the same as (condition A - condition A 
 control), as if subtracting out Contrast 2 had no impact on the map.
 
 Thanks,
 
 Paula
 
 
 
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>>> 
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>>>  
>>> 
>> 
>> 
>> 
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Re: [Freesurfer] Help with mergecontrasts-sess function

[Douglas N. Greve]

There is not a summary table, it is just a map. Do you want a cluster table?

On 11/10/2020 11:26 AM, Paula Maldonado wrote:


External Email - Use Caution

Thanks for your reply, that worked. Can you please tell me where I can 
find a summary table of the activated regions resulting from the 
conjunction analysis?


Best regards,

Paula




Il giorno 27 ott 2020, alle ore 22:50, Douglas N. Greve 
mailto:dgr...@mgh.harvard.edu>> ha scritto:


You would just run mkcontrast-sess, eg, if your four conditions are
ordered condA, condAcontrol, condB, condBcont, then
mkcontrast-sess -analysis analysis -contrast contrastname -a 1 -c 2 -c 3
-a 4
If you want it reversed, then just reverse the a's and c's

On 10/23/2020 4:39 AM, Paula Maldonado wrote:

External Email - Use Caution

Dear experts,
I am running an fMRI experiment in which I have four conditions: two 
main conditions (condition A and condition B) and two respective 
control conditions (condition Acontrol and condition Bcontrol).
I would like to create a map showing significantly greater activity 
for condition A relative to condition B, after subtracting out the 
activity for the respective control conditions. In other words, I 
would like to perform the following contrast:
(condition A - condition A control) - (condition B - condition B 
control)
Then I would like to have a map that shows the reverse contrast 
too:(condition B - condition B control) - (condition A - condition A 
control).


How do I do that?To obtain the first map: (condition A - condition A 
control) - (condition B - condition B control) I have tried with the 
mergecontrasts-sess function with the -conjunction flag and the OR 
option as detailed below:
mergecontrasts-sess -mergedcontrast conjres -conjunction or 
-analysis analysisname -map sig -space sph -isxavg fixed -contrast 
Contrast1 2 pos 0 -contrast Contrast 2 pos 0 -s 
sessionsfMRI/Sub01/bold -hemi lh


where Contrast1= (condition A - condition A control) and Contrast2= 
(condition B - condition B control)
however the map I get is exactly the same as (condition A - 
condition A control), as if subtracting out Contrast 2 had no impact 
on the map.


Thanks,

Paula



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[Freesurfer] Help with MRI labels

[Alberto Del Cerro Leon]

External Email - Use Caution

Good afternoon, my name is Alberto del Cerro and I am a PhD student in the
cognitive and computational neuroscience laboratory (LNCyC) at the
biomedical technology center (CTB) of the Polytechnic University of Madrid
(UPM). I am currently extracting the structural data from the T1 images of
my project and I would like to extract the volume, thickness and curvature
data in the regions of interest where I obtained results in
electrophysiology (MEG). The point is that for this data I used the AAL
atlas and I would like to use these regions to obtain structural data in
FreeSurfer. Researching on the internet I have read that this is possible
with the mri_label2vol command but I would like to know how I can proceed
to obtain this data. Can you guide me in this process?
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Re: [Freesurfer] Help with mergecontrasts-sess function

[Paula Maldonado]

External Email - Use Caution

Thanks for your reply, that worked. Can you please tell me where I can find a 
summary table of the activated regions resulting from the conjunction analysis?

Best regards,

Paula




> Il giorno 27 ott 2020, alle ore 22:50, Douglas N. Greve 
>  ha scritto:
> 
> You would just run mkcontrast-sess, eg, if your four conditions are 
> ordered condA, condAcontrol, condB, condBcont, then
> mkcontrast-sess -analysis analysis -contrast contrastname -a 1 -c 2 -c 3 
> -a 4
> If you want it reversed, then just reverse the a's and c's
> 
> On 10/23/2020 4:39 AM, Paula Maldonado wrote:
>> External Email - Use Caution
>> 
>> Dear experts,
>> I am running an fMRI experiment in which I have four conditions: two main 
>> conditions (condition A and condition B) and two respective control 
>> conditions (condition Acontrol and condition Bcontrol).
>> I would like to create a map showing significantly greater activity for 
>> condition A relative to condition B, after subtracting out the activity for 
>> the respective control conditions. In other words, I would like to perform 
>> the following contrast:
>> (condition A - condition A control) - (condition B - condition B control)
>> Then I would like to have a map that shows the reverse contrast 
>> too:(condition B - condition B control) - (condition A - condition A 
>> control).
>> 
>> How do I do that?To obtain the first map: (condition A - condition A 
>> control) - (condition B - condition B control) I have tried with the 
>> mergecontrasts-sess function with the -conjunction flag and the OR option as 
>> detailed below:
>> mergecontrasts-sess -mergedcontrast conjres -conjunction or -analysis 
>> analysisname -map sig -space sph -isxavg fixed -contrast Contrast1 2 pos 0 
>> -contrast Contrast 2 pos 0 -s sessionsfMRI/Sub01/bold -hemi lh
>> 
>> where Contrast1= (condition A - condition A control) and Contrast2= 
>> (condition B - condition B control)
>> however the map I get is exactly the same as (condition A - condition A 
>> control), as if subtracting out Contrast 2 had no impact on the map.
>> 
>> Thanks,
>> 
>> Paula
>> 
>> 
>> 
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Re: [Freesurfer] Help with mergecontrasts-sess function

[Douglas N. Greve]

You would just run mkcontrast-sess, eg, if your four conditions are 
ordered condA, condAcontrol, condB, condBcont, then
mkcontrast-sess -analysis analysis -contrast contrastname -a 1 -c 2 -c 3 
-a 4
If you want it reversed, then just reverse the a's and c's

On 10/23/2020 4:39 AM, Paula Maldonado wrote:
>  External Email - Use Caution
>
> Dear experts,
> I am running an fMRI experiment in which I have four conditions: two main 
> conditions (condition A and condition B) and two respective control 
> conditions (condition Acontrol and condition Bcontrol).
> I would like to create a map showing significantly greater activity for 
> condition A relative to condition B, after subtracting out the activity for 
> the respective control conditions. In other words, I would like to perform 
> the following contrast:
> (condition A - condition A control) - (condition B - condition B control)
> Then I would like to have a map that shows the reverse contrast 
> too:(condition B - condition B control) - (condition A - condition A control).
>
> How do I do that?To obtain the first map: (condition A - condition A control) 
> - (condition B - condition B control) I have tried with the 
> mergecontrasts-sess function with the -conjunction flag and the OR option as 
> detailed below:
> mergecontrasts-sess -mergedcontrast conjres -conjunction or -analysis 
> analysisname -map sig -space sph -isxavg fixed -contrast Contrast1 2 pos 0 
> -contrast Contrast 2 pos 0 -s sessionsfMRI/Sub01/bold -hemi lh
>
> where Contrast1= (condition A - condition A control) and Contrast2= 
> (condition B - condition B control)
> however the map I get is exactly the same as (condition A - condition A 
> control), as if subtracting out Contrast 2 had no impact on the map.
>
> Thanks,
>
> Paula
>
>
>
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Re: [Freesurfer] Help to create flattened images of a whole hemisphere

[Wang, Ruopeng]

Hi Ornaith,

Regarding your freeview question - you can use shift + Ctrl + left button to 
select vertex for filling uncut area. But I just found out there is a glitch on 
macOS that prevent that from working. A workaround is to uncheck the Cut 
button, which will quit Cut mode and return to normal viewing mode, then just 
left mouse button to move the 3D cursor to the vertex you want, then check Cut 
button again and finish filling uncut area. I’ll fix this issue asap. May also 
drop the shift + ctrl requirement to make the whole process more intuitive.

Best,
Ruopeng

On Oct 23, 2020, at 5:03 AM, Ornaith O Reilly 
mailto:oreil...@tcd.ie>> wrote:


External Email - Use Caution

Hello Freesurfer developers,

I am new to Freesurfer and I'm hoping that someone can help me; I'm attempting 
to get a flattened patch of an entire hemisphere.  Below is a page outlining 
how to use mris_flatten to achieve this:

https://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferOccipitalFlattenedPatch

I am just trying to achieve this with the tutorial data to start with.

1. First problem is that when I run the command 'tksurferfv bert lh inflated'; 
I am getting the error outlined below:

Ornaiths-MacBook-Air-3:subjects ornaithoreilly$ tksurferfv bert lh inflated
freeview -f 
/Applications/freesurfer/7.1.1/subjects/bert/surf/lh.inflated:curvature=/Applications/freesurfer/7.1.1/subjects/bert/surf/lh.curv
 -viewport 3d
/Applications/freesurfer/7.1.1/bin/fsvglrun: line 20: conditional binary 
operator expected
/Applications/freesurfer/7.1.1/bin/fsvglrun: line 20: syntax error near 
`FS_ALLOW_VGLRUN'
/Applications/freesurfer/7.1.1/bin/fsvglrun: line 20: `if [[ ! -v 
FS_ALLOW_VGLRUN ]]; then'
Ornaiths-MacBook-Air-3:subjects ornaithoreilly$


2.  I realised that I could create a patch using freeview instead of tksurfer.  
However I attempted to follow the instructions on the page above to do this and 
ran into some problems.  Image 2 shows an example of the patch that I created 
but when I attempt to press the Press Fill Uncut Area button  (I tried this 
many times and got the same result) a pop up appeared saying "please move 
cursor to a valid vertex".

3.  However one time I did succeed in making a patch (I don't know what I did 
differently this time?) - see image 4 attached.  I saved it as 
lh.full.patch.3d. When I tried to run the command mris_flatten :
mris_flatten -w 10 lh.full.patch.3d lh.full.flat.patch.3d

I got the output:
Ornaiths-MacBook-Air-3:surf ornaithoreilly$ mris_flatten -w 10 lh.full.patch.3d 
lh.full.flat.patch.3d
using write iterations = 10
reading new surface format patch lh.full.patch.3d with 125717 vertices (94.1% 
of total)
reading original vertex positions...
minimizing metric distortion induced by projection...
MRISunfold() max_passes = 1 ---
tol=2.0e-01, sigma=0.0, host=unkno, nav=1024, nbrs=2, l_nlarea=1.000, 
l_dist=1.000
using quadratic fit line minimization
complete_dist_mat 0
rms 0
smooth_averages 0
remove_neg 0
ico_order 0
which_surface 0
target_radius 0.00
nfields 0
scale 0.00
desired_rms_height -1.00
momentum 0.90
nbhd_size 7
max_nbrs 12
niterations 40
nsurfaces 0
SURFACES 3
flags 0 (0)
use curv 0
no sulc 0
no rigid align 0
mris->nsize 2
mris->hemisphere 0
randomSeed 0


/Users/developer/space_freesurfer/build/tulum/trunk/developer-7.1.1/utils/mrisurf_metricProperties.cpp:9034
 Error opening parms.fp using filename lh.full.flat.patch.3d.out mode w

The version of Freesurfer and the platform that I'm using is outlined below:
1) FreeSurfer version: freesurfer-darwin-macOS-7.1.1-20200811-8b40551
2) Platform: macOS High Sierra 10.13.6 (17G7024)

If anyone could shed some light on any of these errors or suggest an 
alternative method it would be greatly appreciated.

Thanks a lot.

Kind Regards
Ornaith O'Reilly
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[Freesurfer] Help with mergecontrasts-sess function

[Paula Maldonado]

External Email - Use Caution

Dear experts,
I am running an fMRI experiment in which I have four conditions: two main 
conditions (condition A and condition B) and two respective control conditions 
(condition Acontrol and condition Bcontrol).
I would like to create a map showing significantly greater activity for 
condition A relative to condition B, after subtracting out the activity for the 
respective control conditions. In other words, I would like to perform the 
following contrast:
(condition A - condition A control) - (condition B - condition B control)
Then I would like to have a map that shows the reverse contrast too:(condition 
B - condition B control) - (condition A - condition A control).

How do I do that?To obtain the first map: (condition A - condition A control) - 
(condition B - condition B control) I have tried with the mergecontrasts-sess 
function with the -conjunction flag and the OR option as detailed below:
mergecontrasts-sess -mergedcontrast conjres -conjunction or -analysis 
analysisname -map sig -space sph -isxavg fixed -contrast Contrast1 2 pos 0 
-contrast Contrast 2 pos 0 -s sessionsfMRI/Sub01/bold -hemi lh

where Contrast1= (condition A - condition A control) and Contrast2= (condition 
B - condition B control)
however the map I get is exactly the same as (condition A - condition A 
control), as if subtracting out Contrast 2 had no impact on the map.

Thanks, 

Paula



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Re: [Freesurfer] Help with creating contrast matrix - 6 classes and 3 variables

[Douglas N. Greve]

With 6 classes and 3 variables, you will have 24 regression coefficients 
and so 24 items in your contrast matrix (so good, so far). The order will be

1. MaleMaxT-Offset
2. MaleKahn-Offset
3.
4.
5.
6.
7. MaleMaxT-AgeSlope
8
9
10
11
12
13 MaleMaxT-HRSD_Reduction-Slope
14 MaleKahn-HRSD_Reduction-Slope
15
16
17
18 FemaleNone-HRSD_Reduction-Slope
19 MaleMaxT-SessionNumber-Slope
20
...

So all the HRSD_Reduction-Slopevariables are in items 13-18, so you set 
them all to 1 and let the others be 0, which is what you have.


Bottom line: you have done it correctly.

On 10/13/2020 7:52 PM, Paul Dhami wrote:


External Email - Use Caution

Dear Freesurfer community,

I am having trouble with my contrast matrix, and would greatly 
appreciate any help with this.


I have 2 categorical variables, sex (2 levels) and training type (3 
levels).


I also have three (continuous) variables: Age, percentage reduction in 
depression scores, and number of sessions.


I would like to assess the correlation between cortical thickness and 
% reduction in depression scores, while accounting for the effects of 
sex, training type, age, and number of sessions as nuisance variables.


Below is 1) my command line, 2) the FSGD fiile, and 3) the design matrix

1.

mri_glmfit.bin --y MDD-lh-thickness.mgh --fsgd 
Reduction_Correlation.fsgd.txt --C 
ME_ReductionCorrelation_Contrast.txt --fwhm 20 --surf fsaverage lh 
--glmdir /Users/prabhjotdhami/Desktop/CorticalThickness/Data/myGLM



2.


GroupDescriptorFile 1
Title MDD_correlation
Class MaleMaxT
Class MaleKahn
Class MaleNone
Class FemaleMaxT
Class FemaleKahn
Class FemaleNone
Variables Age HRSD_Reduction SessionNumber
Input yct-001 FemaleMaxT 24 62.5 20
Input yct-002 MaleKahn 18 70 20
Input yct-004 MaleMaxT 21 50 20
Input yct-005 MaleMaxT 24 25 20
Input yct-006 FemaleKahn 24 65.2173913 20
Input yct-012 FemaleKahn 17 71.42857143 20
Input yct-013 MaleMaxT 22 53.84615385 20
Input yct-014 FemaleMaxT 19 63.63636364 20
Input yct-015 FemaleMaxT 16 80.95238095 20
Input yct-016 FemaleKahn 24 65.2173913 20
Input yct-017 FemaleKahn 22 55 20
Input yct-018 FemaleMaxT 18 82.60869565 20
Input yct-019 MaleKahn 16 85 20
Input yct-020 FemaleMaxT 22 85 20
Input yct-021 MaleMaxT 24 81.81818182 20
Input yct-022 FemaleKahn 21 70.8333 20
Input yct-023 FemaleMaxT 20 52 20
Input yct-024 MaleKahn 16 73.68421053 20
Input yct-025 MaleKahn 21 23.80952381 20
Input yct-026 FemaleMaxT 20 78.26086957 20
Input yct-027 FemaleMaxT 17 20 20
Input yct-030 FemaleMaxT 19 52 20
Input yd-p002 MaleNone 20 54.54545455 10
Input yd-p006 FemaleNone 23 30 10
Input yd-p008 MaleNone 22 44 10
Input yd-p010 FemaleNone 16 50 10
Input yd-p014 FemaleNone 22 3.846153846 10
Input yd-p015 MaleNone 19 10 10
Input yd-p022 FemaleNone 24 37.03703704 10
Input yd-p026 FemaleNone 21 47.61904762 10
Input yd-p027 MaleNone 23 31.57894737 10
Input yd-p032 FemaleNone 21 75 10
Input yd-p033 MaleNone 24 22. 10
Input yd-p034 FemaleNone 22 25 10
Input yd-p035 MaleNone 24 30.43478261 10
Input yd-p047 MaleNone 16 78.26086957 10
Input yd-p048 MaleNone 17 20 10
Input yd-p051 FemaleNone 18 45 10
Input yd-p052 FemaleNone 20 47.82608696 10


3.

0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 1 1 1 0 0 0 0 0 0


Any help would be greatly appreciated.


Thank you,

Paul



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Re: [Freesurfer] Help!

[Yendiki, Anastasia]

What version of FSL are you using? It seems to be an incompatibility between 
the version of FSL and version of python that you have:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=fsl;73e3d6df.1604

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Samar Fouda 

Sent: Friday, October 16, 2020 6:04 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Help!


External Email - Use Caution

Hi Anastasia,

Thank you so much for responding, please find the log attached!

On Fri, Oct 16, 2020 at 3:24 PM Yendiki, Anastasia 
mailto:ayend...@mgh.harvard.edu>> wrote:
Hi Samar - Can you please attach your trac-all.log file and your configuration 
file? It's hard to guess what's going on just from the line where the error 
occurs without seeing everything that came before it.

Thanks!
Anastasia.

From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Samar Fouda mailto:samarsfo...@gmail.com>>
Sent: Friday, October 16, 2020 10:00 AM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: [Freesurfer] Help!


External Email - Use Caution

Hi! I am trying to run tracula- TRAC-All and I get this error message, i 
assumed it is because that bvals and bvecs needed to be predetermined but it 
seems like that is not the case and i am still getting the same error:

Transform file should be eddy_correct/eddy log file or .mat file

What do you think the problem is?

Thanks so much for your help.
--

--

Samar Fouda

Post Doctoral Associate

Emerge Research Program

National Center for PTSD, Clinical Neuroscience Division

Yale School of Medicine

samar.fo...@yale.edu<mailto:samar.fo...@yale.edu>

+1203285-7568

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--

--

Samar Fouda

Post Doctoral Associate

Emerge Research Program

National Center for PTSD, Clinical Neuroscience Division

Yale School of Medicine

samar.fo...@yale.edu<mailto:samar.fo...@yale.edu>

+1203285-7568
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Re: [Freesurfer] Help!

[Samar Fouda]

External Email - Use Caution

Hi Anastasia,

Thank you so much for responding, please find the log attached!

On Fri, Oct 16, 2020 at 3:24 PM Yendiki, Anastasia 
wrote:

> Hi Samar - Can you please attach your trac-all.log file and your
> configuration file? It's hard to guess what's going on just from the line
> where the error occurs without seeing everything that came before it.
>
> Thanks!
> Anastasia.
> --
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
> freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Samar Fouda <
> samarsfo...@gmail.com>
> *Sent:* Friday, October 16, 2020 10:00 AM
> *To:* freesurfer@nmr.mgh.harvard.edu 
> *Subject:* [Freesurfer] Help!
>
>
> External Email - Use Caution
>
> Hi! I am trying to run tracula- TRAC-All and I get this error message, i
> assumed it is because that bvals and bvecs needed to be predetermined but
> it seems like that is not the case and i am still getting the same error:
>
> Transform file should be eddy_correct/eddy log file or .mat file
>
> What do you think the problem is?
>
> Thanks so much for your help.
> --
>
> *--*
>
> *Samar Fouda*
>
> *Post Doctoral Associate*
>
> *Emerge Research Program*
>
> *National Center for PTSD, Clinical Neuroscience Division*
>
> *Yale School of Medicine*
>
> *samar.fo...@yale.edu *
>
> *+1203285-7568*
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer



-- 

*--*

*Samar Fouda*

*Post Doctoral Associate*

*Emerge Research Program*

*National Center for PTSD, Clinical Neuroscience Division*

*Yale School of Medicine*

*samar.fo...@yale.edu *

*+1203285-7568*


trac-all.log
Description: Binary data
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Re: [Freesurfer] Help!

[Yendiki, Anastasia]

Hi Samar - Can you please attach your trac-all.log file and your configuration 
file? It's hard to guess what's going on just from the line where the error 
occurs without seeing everything that came before it.

Thanks!
Anastasia.

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Samar Fouda 

Sent: Friday, October 16, 2020 10:00 AM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: [Freesurfer] Help!


External Email - Use Caution

Hi! I am trying to run tracula- TRAC-All and I get this error message, i 
assumed it is because that bvals and bvecs needed to be predetermined but it 
seems like that is not the case and i am still getting the same error:

Transform file should be eddy_correct/eddy log file or .mat file

What do you think the problem is?

Thanks so much for your help.
--

--

Samar Fouda

Post Doctoral Associate

Emerge Research Program

National Center for PTSD, Clinical Neuroscience Division

Yale School of Medicine

samar.fo...@yale.edu<mailto:samar.fo...@yale.edu>

+1203285-7568
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[Freesurfer] Help!

[Samar Fouda]

External Email - Use Caution

Hi! I am trying to run tracula- TRAC-All and I get this error message, i
assumed it is because that bvals and bvecs needed to be predetermined but
it seems like that is not the case and i am still getting the same error:

Transform file should be eddy_correct/eddy log file or .mat file

What do you think the problem is?

Thanks so much for your help.
-- 

*--*

*Samar Fouda*

*Post Doctoral Associate*

*Emerge Research Program*

*National Center for PTSD, Clinical Neuroscience Division*

*Yale School of Medicine*

*samar.fo...@yale.edu *

*+1203285-7568*
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[Freesurfer] Help with creating contrast matrix - 6 classes and 3 variables

[Paul Dhami]

External Email - Use Caution

Dear Freesurfer community,

I am having trouble with my contrast matrix, and would greatly appreciate
any help with this.

I have 2 categorical variables, sex (2 levels) and training type (3
levels).

I also have three (continuous) variables: Age, percentage reduction in
depression scores, and number of sessions.

I would like to assess the correlation between cortical thickness and %
reduction in depression scores, while accounting for the effects of sex,
training type, age, and number of sessions as nuisance variables.

Below is 1) my command line, 2) the FSGD fiile, and 3) the design matrix

1.

mri_glmfit.bin --y MDD-lh-thickness.mgh --fsgd
Reduction_Correlation.fsgd.txt --C ME_ReductionCorrelation_Contrast.txt
--fwhm 20 --surf fsaverage lh --glmdir
/Users/prabhjotdhami/Desktop/CorticalThickness/Data/myGLM


2.


GroupDescriptorFile 1
Title MDD_correlation
Class MaleMaxT
Class MaleKahn
Class MaleNone
Class FemaleMaxT
Class FemaleKahn
Class FemaleNone
Variables Age HRSD_Reduction SessionNumber
Input yct-001 FemaleMaxT 24 62.5 20
Input yct-002 MaleKahn 18 70 20
Input yct-004 MaleMaxT 21 50 20
Input yct-005 MaleMaxT 24 25 20
Input yct-006 FemaleKahn 24 65.2173913 20
Input yct-012 FemaleKahn 17 71.42857143 20
Input yct-013 MaleMaxT 22 53.84615385 20
Input yct-014 FemaleMaxT 19 63.63636364 20
Input yct-015 FemaleMaxT 16 80.95238095 20
Input yct-016 FemaleKahn 24 65.2173913 20
Input yct-017 FemaleKahn 22 55 20
Input yct-018 FemaleMaxT 18 82.60869565 20
Input yct-019 MaleKahn 16 85 20
Input yct-020 FemaleMaxT 22 85 20
Input yct-021 MaleMaxT 24 81.81818182 20
Input yct-022 FemaleKahn 21 70.8333 20
Input yct-023 FemaleMaxT 20 52 20
Input yct-024 MaleKahn 16 73.68421053 20
Input yct-025 MaleKahn 21 23.80952381 20
Input yct-026 FemaleMaxT 20 78.26086957 20
Input yct-027 FemaleMaxT 17 20 20
Input yct-030 FemaleMaxT 19 52 20
Input yd-p002 MaleNone 20 54.54545455 10
Input yd-p006 FemaleNone 23 30 10
Input yd-p008 MaleNone 22 44 10
Input yd-p010 FemaleNone 16 50 10
Input yd-p014 FemaleNone 22 3.846153846 10
Input yd-p015 MaleNone 19 10 10
Input yd-p022 FemaleNone 24 37.03703704 10
Input yd-p026 FemaleNone 21 47.61904762 10
Input yd-p027 MaleNone 23 31.57894737 10
Input yd-p032 FemaleNone 21 75 10
Input yd-p033 MaleNone 24 22. 10
Input yd-p034 FemaleNone 22 25 10
Input yd-p035 MaleNone 24 30.43478261 10
Input yd-p047 MaleNone 16 78.26086957 10
Input yd-p048 MaleNone 17 20 10
Input yd-p051 FemaleNone 18 45 10
Input yd-p052 FemaleNone 20 47.82608696 10


3.

0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 1 1 1 0 0 0 0 0 0


Any help would be greatly appreciated.


Thank you,

Paul
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Re: [Freesurfer] Help with LGI

[Lab of Autism and Developmental Neuroscience, Lab of Autism and Developmental Neuroscience]

External Email - Use Caution

Dear Tim,

1) Here is the output after I type matlab:
- Matlab does open, and the following appears on terminal:
shell-init: error retrieving current directory: getcwd: cannot access
parent directories: No such file or directory
pwd: error retrieving current directory: getcwd: cannot access parent
directories: No such file or directory
pwd: error retrieving current directory: getcwd: cannot access parent
directories: No such file or directory
chdir: error retrieving current directory: getcwd: cannot access parent
directories: No such file or directory
GVA encoder info: AMD performance mode : 2
GVA encoder info: deleteSCDMetalContext : texture cache hits: 0, misses: 0

2) and /Applications/MATLAB_R2020a/bin/matlab:
/Applications/MATLAB_R2020a/bin/matlab: No such file or directory

Please let me know if you need more information.

Thank you,
Alex


On Wed, Aug 5, 2020 at 3:42 AM Tim Schäfer  wrote:

> External Email - Use Caution
>
> Looks like something is wrong with the Matlab installation. It would be
> good to know:
>
> 1) What happens if you type 'matlab' in your shell?
> 2) What happens if you type '/Applications/MATLAB_R2020a/bin/matlab' in
> your shell?
>
> Best,
>
> Tim
>
> > On August 4, 2020 at 8:31 PM "Lab of Autism and Developmental
> Neuroscience, Lab of Autism and Developmental Neuroscience" <
> l...@email.gwu.edu> wrote:
> >
> >
> > External Email - Use Caution
> >
> > Dear Freesurfer experts,
> >
> > Just wanted to follow up my last email - does anyone know what might be
> > wrong with my code?
> >
> > Thank you and stay safe,
> > Alex
> >
> > On Sat, Aug 1, 2020 at 5:40 PM Lab of Autism and Developmental
> > Neuroscience, Lab of Autism and Developmental Neuroscience <
> > l...@email.gwu.edu> wrote:
> >
> > > Dear Douglas,
> > >
> > > Yes, now matlab is correctly set to my freesurfer path, but the
> following
> > > error occurs when I run localGI (please see below). Any ideas what
> might be
> > > wrong? Maybe there are some issues with the matlab version or image
> > > processing toolbox that I'm using?
> > >
> > > iMac-Pro:BAP_complete ajobsaid$ recon-all -s nih00024_epoch11_4
> -localGI
> > > Subject Stamp: freesurfer-darwin-macOS-7.1.0-20200511-813297b
> > > Current Stamp: freesurfer-darwin-macOS-7.1.0-20200511-813297b
> > > INFO: SUBJECTS_DIR is /Applications/BAP_complete
> > > Actual FREESURFER_HOME /Applications/freesurfer
> > > -rw-rw-r--  1 ajobsaid  982768932  956144 Jun 30 09:20
> > > /Applications/BAP_complete/nih00024_epoch11_4/scripts/recon-all.log
> > > Darwin iMac-Pro.local 19.6.0 Darwin Kernel Version 19.6.0: Sun Jul  5
> > > 00:43:10 PDT 2020; root:xnu-6153.141.1~9/RELEASE_X86_64 x86_64
> > > /Applications/BAP_complete/nih00024_epoch11_4/mri/transforms
> > > /Applications/BAP_complete/nih00024_epoch11_4
> > > /Applications/BAP_complete/nih00024_epoch11_4
> > > #@# white curv lh Fri Jul 31 09:20:05 PDT 2020
> > > cd /Applications/BAP_complete/nih00024_epoch11_4/mri
> > > mris_place_surface --curv-map ../surf/lh.white 2 10 ../surf/lh.curv
> > >Update not needed
> > > #@# white area lh Fri Jul 31 09:20:05 PDT 2020
> > > cd /Applications/BAP_complete/nih00024_epoch11_4/mri
> > > mris_place_surface --area-map ../surf/lh.white ../surf/lh.area
> > >Update not needed
> > > #@# pial curv lh Fri Jul 31 09:20:05 PDT 2020
> > > cd /Applications/BAP_complete/nih00024_epoch11_4/mri
> > > mris_place_surface --curv-map ../surf/lh.pial 2 10 ../surf/lh.curv.pial
> > >Update not needed
> > > #@# pial area lh Fri Jul 31 09:20:05 PDT 2020
> > > cd /Applications/BAP_complete/nih00024_epoch11_4/mri
> > > mris_place_surface --area-map ../surf/lh.pial ../surf/lh.area.pial
> > >Update not needed
> > > #@# thickness lh Fri Jul 31 09:20:05 PDT 2020
> > > cd /Applications/BAP_complete/nih00024_epoch11_4/mri
> > > mris_place_surface --thickness ../surf/lh.white ../surf/lh.pial 20 5
> > > ../surf/lh.thickness
> > >Update not needed
> > > #@# area and vertex vol lh Fri Jul 31 09:20:05 PDT 2020
> > > cd /Applications/BAP_complete/nih00024_epoch11_4/mri
> > > mris_place_surface --thickness ../surf/lh.white ../surf/lh.pial 20 5
> > > ../surf/lh.thickness
> > >Update not needed
> > > #@# white curv rh Fri Jul 31 09:20:05 PDT 2020
> > > cd /Applications/BAP_complete/nih00024_epoch11_4/mri
> > > mris_place_surface --curv-map ../surf/rh.white 2 10 ../surf/rh.curv
> > >Update not needed
> > > #@# white area rh Fri Jul 31 09:20:05 PDT 2020
> > > cd /Applications/BAP_complete/nih00024_epoch11_4/mri
> > > mris_place_surface --area-map ../surf/rh.white ../surf/rh.area
> > >Update not needed
> > > #@# pial curv rh Fri Jul 31 09:20:05 PDT 2020
> > > cd /Applications/BAP_complete/nih00024_epoch11_4/mri
> > > mris_place_surface --curv-map ../surf/rh.pial 2 10 ../surf/rh.curv.pial
> > >Update not needed
> > > #@# pial area rh Fri Jul 31 09:20:05 PDT 2020
> > > cd /Applications/BAP_complete/nih00024_epoch11_4/mri
> > >