To mimic the original matlab implementation, segment_subregions saves stats as
*.txt files in the mri subdirectory of the subject.
But maybe we should just save things in the stats folder to be consistent.
Eugenio/Doug, what do you think?
Andrew
From: freesurfer-boun...@nmr.mgh.harvard.edu
o
Unfortunately, tensorflow and M1 don’t mix well at the moment. Not sure if
there is a universal fix yet.
Rob, do you remember where the mac-specific TF package can be installed from?
Best,
Andrew
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Abdelkarim, Ahmed
Date: Tuesday, July
This might be related to a small bug in the previous longitudinal code, which
affected volume rescaling. It should be fixed now. You could try out the new
implementation: https://surfer.nmr.mgh.harvard.edu/fswiki/SubregionSegmentation
Best,
Andrew
From: freesurfer-boun...@nmr.mgh.harvard.edu
External Email - Use Caution
Tried it, but I still get the same error.
--
Caitlin Bowman, Ph.D.
Assistant Professor of Psychology
University of Wisconsin-Milwaukee
From: on behalf of "Hoopes, Andrew"
Reply-To: Freesurfer support list
Date: Tuesday, March 8, 2022 at 3:18 PM
To:
Hi Randy,
As Koen mentioned, FS support for ushort file types wasn’t added until
recently. I just extended that support to the python (samseg) tools yesterday,
so this should work in the most recent development (nightly) freesurfer
distributions. You could install that, or you could convert you
Hi Begum,
You could try the just-recently released SynthStrip command `mri_synthstrip`
available in the dev distributions of freesurfer (as of today, march 15th). It
should be more robust than the watershed utility.
Best,
Andrew
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Begüm
Hi Cait,
Before running the command, can you try unsetting the LD_LIBRARY_PATH variable?
You can do this in bash with:
unset LD_LIBRARY_PATH
or in cshell with:
unsetenv LD_LIBRARY_PATH
best,
Andrew
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Caitlin R Bowman
Date: Tuesday,
Hi Randy,
I agree with Stefano that this is likely due to your CPU not supporting AVX
instructions, since this is not a reproducible error when running VM 67 on our
mac and linux test machines. Here’s some more info:
https://github.com/tensorflow/tensorflow/issues/46108
Unfortunately, there is
Hi Corinna,
Do you happen to have the LD_LIBRARY_PATH environment variable set in your
shell? If so, I would unset it. LD_LIBRARY_PATH tends to mess with any programs
linked to dynamic libraries. In this case, it’s forcing freeview to load the
wrong matlab Qt libraries.
Andrew
From: freesurfer-
Are you adding sudo in front of every command? like this:
cd $FREESURFER_HOME/bin && sudo curl
https://raw.githubusercontent.com/freesurfer/freesurfer/dev/scripts/fs_install_mcr
-o fs_install_mcr && sudo chmod +x fs_install_mcr
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Junyeon
Yes! And thanks for the reminder – I just pushed 7.2.0 to dockerhub
Andrew
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Andy Worth
Date: Tuesday, August 31, 2021 at 3:45 PM
To: Freesurfer support list
Subject: [Freesurfer] Shiny new 7.2!
External Email - Use Caution
Is i
container instead?
https://hub.docker.com/r/freesurfer/freesurfer
Best
Andrew
From: Iglesias Gonzalez, Juan E.
Date: Thursday, August 12, 2021 at 2:57 PM
To: Freesurfer support list
Cc: Hoopes, Andrew
Subject: Re: [Freesurfer] Hippocampal, thalamus and brainstem subfields: Matlab
crash bump
Hi Lauri,
This is fixed in v7.2, but if you want to patch your current freesurfer
distribution, you can try these commands:
cd $FREESURFER_HOME/bin
sudo mv fsvglrun fsvglrun.backup
sudo curl -O
https://raw.githubusercontent.com/freesurfer/freesurfer/dev/scripts/fsvglrun
sudo chmod +x fsvglrun
This is fixed in v7.2, but if you want to patch your current freesurfer
distribution, you can try these commands:
cd $FREESURFER_HOME/bin
sudo mv fsvglrun fsvglrun.backup
sudo curl -O
https://raw.githubusercontent.com/freesurfer/freesurfer/dev/scripts/fsvglrun
sudo chmod +x fsvglrun
best
Andrew
Hi Xin,
Are you using the QA tools from
https://surfer.nmr.mgh.harvard.edu/fswiki/QATools? Those are specific to FS 5.3
(we should update the wiki). v7.1 includes an executable named `qatools.py`
that functions similarly.
best
Andrew
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of
Hi Rito, which freesurfer version are you using here?
Andrew
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Ritobrato Datta
Date: Wednesday, August 11, 2021 at 3:01 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] error running samseg on cluster
External Email -
We don’t release the fsaverage subject alone. You might be able to work some
magic with the curl and tar commands to pull and extract just the fsaverage
subdirectory from a freesurfer release archive, but I’m not sure how (or if)
that can be done. Plus, it still probably requires downloading mos
The line of code you sent doesn’t seem changed though
best
andrew
From: Kaija Sander
Date: Thursday, July 29, 2021 at 5:40 PM
To: Hoopes, Andrew , Freesurfer support list
Cc: Iglesias Gonzalez, Juan E.
Subject: Re: [Freesurfer] Error in hippocampal subfields longitudinal processing
Hi Kaija,
Not sure I follow. Have you tried making the change I suggested in the last
email?
Best,
Andrew
From: Kaija Sander
Date: Wednesday, July 28, 2021 at 2:30 PM
To: Freesurfer support list
Cc: Hoopes, Andrew , Iglesias Gonzalez, Juan E.
Subject: Re: [Freesurfer] Error in hippocampal
Hi Kaija,
I believe this is related to limitations in temporary file handling. You could
try manually replacing the MCR_CACHE_ROOT path on line 49 of:
$FREESURFER_HOME/bin/run_SegmentSubfieldsT1Longitudinal.sh
With something like:
MCR_CACHE_ROOT=$( echo "$HOME/MCR_${RANDOMNUMBER}/" | tr -d ' '
ORTEGA CRUZ <100315...@alumnos.uc3m.es>
Date: Thursday, May 27, 2021 at 3:32 AM
To: Freesurfer support list , Hoopes, Andrew
Subject: Re: [Freesurfer] Recon-all running on a loop
External Email - Use Caution
Dear Andrew,
Thank you for your reply. I shared with you the recon-all.cm
Hi Nárlon,
There’s no harm in installing multiple versions of freesurfer on one
filesystem. The FS distribution is confined to the directory it’s installed to,
so we suggest organizing a FREESURFER_HOME directory structure like:
/Applications/freesurfer/5.3
/Applications/freesurfer/6.0
/Applica
Hi Diana,
Can you send the recon-all.cmd file? Have you tried running without parallel
processing enabled?
Best,
Andrew
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of DIANA ORTEGA CRUZ
<100315...@alumnos.uc3m.es>
Date: Friday, May 21, 2021 at 11:00 AM
To: freesurfer@nmr.mgh.harvar
Hi Joe,
Is this the full command output from start to finish? There is usually some
helpful information preceding the “Segmentation violation detected” error.
Best
Andrew
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Xin Qiao
Date: Thursday, May 20, 2021 at 12:44 AM
To: freesurf
Hi Joana,
I agree with Eugenio that if this is failing from within python, then python is
probably messing with your environment. Based on that error log, it’s tough to
say whether this is a freesurfer problem or matlab. The fact that it runs fine
on linux seems to suggest it’s a macOS-specific
Hi Erika,
Can you untar the file you downloaded instead of the "HighSierra" version.
There was a small typo in the UpdateFreeview instructions that mentioned
high-sierra. The freeview you downloaded should work fine for 10.12
Best,
Andrew
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behal
Hi Fabio,
How much memory are you allowing for this process? You might want to just try
increasing the limit on the slurm job to see if that works.
Best
Andrew
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Bernardoni, Fabio
Date: Tuesday, May 11, 2021 at 4:22 AM
To: freesurfer m
of 171720 exceeds 10% of system memory.
I tried to improve the system memory of my virtual machine but the same error
appeared.
Any suggestions?
El vie, 7 may 2021 a las 20:59, Hoopes, Andrew
(mailto:ahoo...@mgh.harvard.edu>>) escribió:
If the output directory is missing seg.mgz
Hi Melissa,
If the command runs fine in the terminal but not from python, it’s most likely
because python is messing with aspects of your env before running commands in a
subshell. The easiest solution is to upgrade to FS v7, where this problem no
longer exists, but if you’re stuck at v6, you s
urfer-boun...@nmr.mgh.harvard.edu
on behalf of Hoopes, Andrew
Sent: Friday, May 7, 2021 5:01 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] Freesurfer 7 crashes during mris_fix_topology
Hi Renat,
The third defect is too large and it’s causing a crash. When I run it, it hangs
forever at:
If the output directory is missing seg.mgz, then samseg failed. You’ll have to
send us the log or some sort of information about the error for us to debug
this.
Best
Andrew
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Alberto Del Cerro Leon
Date: Friday, May 7, 2021 at 6:49 AM
Hi Giulio,
I’ll follow up off-list.
Andrew
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Giulio Degano
Date: Friday, May 7, 2021 at 3:20 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Multiple Freesurfer(s)
External Email - Use Caution
Hi all,
I am trying to
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
Hi Jewelia,
Can you try running without the -parallel flag to see if that’s the issue?
Best
Andrew
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Jewelia K. Yao
Date: Tuesday, May 4, 2021 at 11:06 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Freesurfer version 7 re
Hi Renat,
That 3rd defect is fairly large – normally it would hang but it’s possible
you’re running out of memory. If you can zip the subject and file drop it to
us, we can take a look:
https://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange
best,
Andrew
From: freesurfer-boun...@nmr.mgh.har
Hi Mudathir,
What freesurfer version are using? I haven’t been able to reproduce this
segfault on our end. Can you run the same command on lh.aparc.annot instead to
narrow down whether this is an issue with your lh.par.annot file or not?
best
Andrew
From: freesurfer-boun...@nmr.mgh.harvard.edu
Hi Josephine,
It appears that the rh.thickness file is corrupted. I would suggest rerunning
to see if that clears things up.
Andrew
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of 林諐庭
Date: Tuesday, April 20, 2021 at 4:35 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer]
Please check out the known issues section of
https://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes for a fix
Best,
Andrew
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Vishnu S
Date: Monday, April 19, 2021 at 8:05 AM
To: Freesurfer support list
Subject: [Freesurfer] Freeview -
Hi Christina,
You’ll need to specify the version tag. You can try:
docker pull freesurfer/freesurfer:7.1.1
best,
Andrew
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Chr. Roßmanith
Date: Friday, April 16, 2021 at 8:41 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer]
Hi AJ,
Freesurfer ships its own python distribution, so it doesn’t matter what you
have installed on your system. Can you let us know the specific version of
macOS you are using and send the full error report from pip?
Thanks
Andrew
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of A
Hi Max,
You could try downloading an updated, standalone release of freeview from
https://surfer.nmr.mgh.harvard.edu/fswiki/UpdateFreeview
Best,
Andrew
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Max Korbmacher
Date: Wednesday, April 14, 2021 at 2:05 PM
To: freesurfer@nmr.mgh.
Hi Phillip,
Yes, 5.3 is getting to the point where some components are just too old to
install correctly on modern system. I would read through this thread
https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg69376.html that
discusses this problem and a potential solution, similar to
I’m not totally sure of the answer here. Could be filesystem limitations or a
permissions issue. Have you tried untar’ing without the -p flag, or ensuring
that you can write to /usr/local?
Best
Andrew
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Pål Gunnar Larsson
Date: Tuesday
Have you made sure that you have read permission to open those files? What is
the output of `ls -l asta.mgh`? And asta.nii doesn’t seem to be a file in your
working directory.
Best,
Andrew
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Pierpaolo Croce
Date: Thursday, April 8, 202
Thanks for the details. We’ll look into it a bit and get back to you.
Andrew
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Cook, Philip
Date: Monday, April 5, 2021 at 11:42 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] "ERROR: crypt() returned null with 4-line file"
r?
Thanks!
Katja
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Hoopes, Andrew
Sent: Saturday, March 27, 2021 4:19 PM
To: Freesurfer support list
Subject: [External] Re: [Freesurfer] "ERROR: crypt() returned null with 4-line
file" when running
Matt (cc’d) has recently posted a similar error on the last. Unfortunately,
these mac MCR errors are difficult to debug. You could wait for the python
subfield port to get released, but that might be a few months down the line. If
you want to get things running immediately, one thing to try is t
Hi Katja,
I wonder if this is related to possible security settings. I can’t replicate
this, but can you send your license file so that we can narrow down the
possibilities? You can send it directly to my email, off-list.
Best
Andrew
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of
Hi Ezequiel,
Just including the FS license in the software as a separate text file is fine.
Best,
Andrew
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Ezequiel Mikulan
Date: Monday, March 22, 2021 at 12:48 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] License Agree
Hi Ursula,
I was just reminded that we purposely don’t include MCR in the container due to
redistribution-restrictions by the MCR license. So, it’s up to the user to
install or provide the MCR library if needed.
best
Andrew
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Hoopes
Hi Ursula,
Thanks for pointing this out. I think it’s just the case that MCR wasn’t
installed in that container. I’m surprised this hasn’t been brought up before.
We’ll update the container with it.
best
Andrew
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Ursula Tooley
Date: F
Hi Matt,
Hopefully this isn’t specific to M1, but I’m not sure it would be in this case.
Maybe try running fs_install_mcr with sudo in front? Some users are suggesting
it here:
https://www.mathworks.com/matlabcentral/answers/176228-error-message-install_unix-not-found
best
Andrew
From: freesur
quot;
VERSION="8"
ID="centos"
ID_LIKE="rhel fedora"
VERSION_ID="8"
PLATFORM_ID="platform:el8"
PRETTY_NAME="CentOS Linux 8"
ANSI_COLOR="0;31"
CPE_NAME="cpe:/o:centos:centos:8"
HOME_URL="https://centos.org/";
BUG_REPORT
Hi Philipp,
Can you let us know the OS and version you’re running on? The license format
was updated for v6. It should be backwards compatible, but it’s possible it’s
not anymore on newer systems.
thanks
Andrew
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Saemann, Philipp
Date
The 'matlab runtime' (MCR) installed by fs_install_mcr lets you run compiled
matlab binaries, but it’s different from having matlab actually installed on
your system. MCR is used to run the sub-structure segmentation tools, but
mris_compute_lgi is a command that runs matlab scripts directly, so
External Email - Use Caution
External Email - Use Caution
Andrew,
That's a great suggestion, thanks.
Any idea whether using the MNI from FS6 has an impact on the results?
Cheers,
Malcolm
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of H
Hi Malcolm,
Yes, this is an unfortunate bug, but I've been playing around with a few
options and the following seems to be the best patch. This assumes you also
have FS v6 installed and, in this case, FS_53 and FS_60 point to the
respective freesurfer base directories:
rm -rf $FS_53/mni
cp -r
If you installed freesurfer with admin permissions, you should mv or cp the
file to the destination directory with `sudo` in front of your command to run
as root.
Andrew
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Donato Romano
Date: Monday, March 8, 2021 at 6:52 AM
To: freesur
Looks like it downloaded fine. In that case, just move that file to your FS
install:
mv fs_install_mcr $FREESURFER_HOME/bin
and you should be good to go.
Best
Andrew
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Georgia Kapizioni
Date: Monday, March 1, 2021 at 10:57 AM
To: free
Can you run this instead:
apt-get -y install libncurses5
That should fix it. Also, please do not globally add the MCRv84 path to
LD_LIBRARY_PATH. This shouldn’t be needed to run the subfield code and will
likely cause problems for other freesurfer binaries.
Best
Andrew
From: freesurfer-boun..
Hi Bruno,
I’m not sure I fully understand the question. If you want to use freesurfer in
combination with MNE, why not just install FS normally and source it while
you’ve activated your conda environment?
Best
Andrew
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Bruno Mansur
Da
Hi Georgia,
No worries. It just means you’re missing wget, but we should probably figure
out the problem with curl. From any directory, can you run:
curl
https://raw.githubusercontent.com/freesurfer/freesurfer/dev/scripts/fs_install_mcr
-o fs_install_mcr
ls fs_install_mcr
What’s the output of
you,
Michele
On Fri, 12 Feb 2021 at 10:05, Michele Valotti
mailto:michele.valo...@gmail.com>> wrote:
Hi Andrew,
thank you for your help, I have attached the mri_nu_correct log from the base
freesurfer directory, let me know if this helps
Michele
On Thu, 11 Feb 2021 at 17:16, Hoopes,
seems to be stored in the .pial files, though, so
blender may assist in suggesting debugging, but is unlikely to solve the
problem in my estimation.
Thanks for your thoughts,
Mike
On Tue, Feb 16, 2021 at 2:06 PM Hoopes, Andrew
mailto:ahoo...@mgh.harvard.edu>> wrote:
Hi Mike,
Are you
Hi Ishi,
What FS version are you using? Can you try installing `apt-get install
libncurses5-dev`?
Andrew
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Ishi Tandon
Date: Thursday, February 18, 2021 at 12:59 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Hippocampus s
Hi Mike,
Are you loading the STL files or the original pial files in freeview here?
If the former, have you narrowed down whether this is an issue with STL
conversion or the actual surfaces? FS surface files only store vertex and face
data, not normals. So, is it possible the normals are being
- Use Caution
Hi Andrew,
I do think the problem is in the MINC but the minc paths point to the
freesurfer installation, so I think it should be running using that
thank you,
Michele
On Thu, 11 Feb 2021 at 16:29, Hoopes, Andrew
mailto:ahoo...@mgh.harvard.edu>> wrote:
Hi Michele,
I think that
g-Much
Research Associate
McGill University
MD Anderson Cancer Centre
--
From:
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
on behalf of "Hoopes, Andrew"
mailto:ahoo...@mgh.harvard.edu>>
Reply-To: Freesurfer support list
mailto:freesurfer@nmr.mgh.harvard.edu>>
Date:
Can you provide a bit more information about how you installed the license(s)
and what errors you’re encountering?
best
Andrew
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Fernanda Hansen P. de
Moraes
Date: Thursday, February 11, 2021 at 9:45 AM
To: Freesurfer support list
Sub
Can you send the `mri/mri_nu_correct.mni.log` file as well? Have you installed
minc tools separately on your local machine and do you have any of these
variables set in your default environment?
MNI_DIR
MINC_BIN_DIR
MINC_LIB_DIR
It’s possible there’s another install of MNI that’s interfering wi
Hi Georgia,
I think you forgot to run the last word "fs_install_mcr" in that command (after
chmod +x). That’s why chmod is throwing a usage error. That doesn’t solve the
reason why it’s not downloading though. Can you try a different tool, like wget
and let me know if anything downloaded:
wget
Hi Georgia,
If you downloaded the runtime installer script to FREESURFER_HOME, which it
looks like you did, the command should be available to run as long as you’ve
also sourced that version of freesurfer, i.e. $FREESURFER_HOME/bin is in your
PATH.
If this is the case and it still can’t find t
ported ...
Then try running your command again.
- R.
On Feb 5, 2021, at 12:37, Hoopes, Andrew
mailto:ahoo...@mgh.harvard.edu>> wrote:
Yes, this probably has to do with SIP being enabled, which blocks libraries
stored in /usr. This was a pretty common issue that people had with v6.
Hi Francois, just responded on github.
Andrew
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Francois Tadel, Mr
[Affiliate]
Date: Friday, February 5, 2021 at 6:17 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Recommendation for FreeSurfer BIDS derivatives?
Ext
--help: mri_convert:
mri_convert: /lib/x86_64-linux-gnu/libcrypt.so.1: version `XCRYPT_2.0' not
found (required by mri_convert)
On Feb 3, 2021, at 1:04 PM, Hoopes, Andrew wrote:
Thanks. Can you run something like `mri_convert --help` to check if this is an
issue with all the FS binarie
Yes, this probably has to do with SIP being enabled, which blocks libraries
stored in /usr. This was a pretty common issue that people had with v6. You can
try disabling SIP via
http://osxdaily.com/2015/10/05/disable-rootless-system-integrity-protection-mac-os-x
best
Andrew
From: freesurfer-bo
-20200511-813297
Freesurfer DEV: freesurfer-linux-centos8_x86_64-dev-20201109-2e16dca)
-Mackenzie
On Wed, Feb 3, 2021 at 10:37 AM Hoopes, Andrew
mailto:ahoo...@mgh.harvard.edu>> wrote:
Hi Mackenzie,
Can you let us know what OS and version you’re running this on?
Thanks,
Andrew
From:
freesurfe
Hi Mackenzie,
Can you let us know what OS and version you’re running this on?
Thanks,
Andrew
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Langan, Mackenzie
Date: Wednesday, February 3, 2021 at 10:31 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Issue with the hypo
Hi Alex,
After sourcing the dev distribution, can you run:
fspython -m pip install h5py==2.10.0
This is an unfortunate bug with older versions of keras and newer versions of
h5py, but we’ll be upgrading our internal scripts soon to deal with this.
Thanks for point this out - I’ll put a note in
n behalf of "Hoopes, Andrew"
Reply to: Freesurfer support list
Date: Tuesday, 26 January 2021 at 22:05
To: Freesurfer support list
Subject: Re: [Freesurfer] FW: T1 Recon-all error: CTABWriteFileASCII; could not
open file for writing
Okay, maybe it’s a permission error. How about
Hi Ali,
Can you please remove the MCR directory and install it using the instructions
found at https://surfer.nmr.mgh.harvard.edu/fswiki/MatlabRuntime? I think this
will fix the issue.
Best,
Andrew
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Snedden, Ali
Date: Wednesday, Janu
-private-845d4b93c36041db9cb4f47a494a5f87-ntpd.service-ukGmwH
What would you recommend doing?
Thank you.
Best,
Flavia
From: on behalf of "Hoopes, Andrew"
Reply to: Freesurfer support list
Date: Tuesday, 26 January 2021 at 17:32
To: Freesurfer support list
Subject: Re: [Freesurfer] FW: T1 Recon-all error:
Hi Flavia,
Do you have access to /tmp on your system? Can you `ls /tmp`?
Andrew
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Loreto, Flavia
Date: Tuesday, January 26, 2021 at 11:29 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] FW: T1 Recon-all error: CTABWriteFi
Hi Jesper,
It’s a memory error - how much do you have available? Also, what is the size of
your input image? That array shape seems rather large.
Best,
Andrew
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Jesper Folsted Kallehauge
Date: Saturday, January 23, 2021 at 2:26 PM
To:
Hi Michele,
Looks like the base error here is:
ncopen: filename "./tmp.mri_nu_correct.mni.6973/nu1.mnc": Not a netCDF file
My immediate guess is this is a version incompatibility. You mentioned that you
reinstalled minc tools? How so and with what version? Also, what was the
previous nu_correct
Hi Nárlon,
Unfortunately, this is a known bug with parallel processing in FS 7.1.1. A fix
will make it into the next v7 patch. As you mentioned, this error occurs at
random, so in the meantime, you can mitigate this by either:
- Rerunning recons until they don’t fail (not recommended)
-
Hi Jan,
Thanks for pointing this out. We upgraded our server recently, and I think some
files got moved around. Should be fixed now.
Best,
Andrew
From: on behalf of "Sellner, Jan"
Reply-To: FS Help
Date: Tuesday, December 8, 2020 at 11:50 AM
To: FS Help
Subject: [Freesurfer] Error while re
Hi Keith, what version of ubuntu are you using?
Best
Andrew
From: "Iglesias Gonzalez, Juan E."
Date: Friday, December 4, 2020 at 4:42 PM
To: FS Help
Cc: "Hoopes, Andrew"
Subject: Re: [Freesurfer] segmentHA_T1.sh failing {Disarmed}
Dear Keith,
It is a license problem
Hi Noam,
Do the volumes look okay? I’m seeing a lot of ‘non-orthogonal axes’ warnings in
the log. If that’s not the issue, this could be a bug that’s randomly occurring
with parallel recons in v7. Although, I’ve never seen it fail during
mri_convert. Can you try to rerun? It might succeed the s
-Linux-centos6_x86_64-stable-pub-v5.3.0which downloaded from
freesurfer website. The license file was four lines type. Hope this information
is helpful.
Thanks,
Lunhao
From: freesurfer-boun...@nmr.mgh.harvard.edu
代表 Hoopes, Andrew
Date: 2020年11月21日 1:19
Reply-To: Freesurfer support list
Hi Lunhao,
Interesting. Can you provide some details on the configurations where this
worked? Were you using the same linux subsystem and windows versions?
thanks
Andrew
From: on behalf of Shen Lunhao
Reply-To: FS Help
Date: Friday, November 20, 2020 at 2:44 AM
To: FS Help
Subject: [Freesu
re I could access
more information on rsync or moving data to a different location?
That would be super helpful!
Thank you again for your help.
Sincerely,
James Park
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Hoopes, Andrew
Sent: Monday, Octobe
: Monday, October 26, 2020 at 7:29 PM
To: FS Help
Subject: Re: [Freesurfer] Exited with errors, segmentation fault
External Email - Use Caution
Hi,
Thank you for your email. Sorry about that. Here they are.
Best regards,
Julia
> 27 okt. 2020 kl. 00:17 skrev Hoopes, Andrew :
>
>
020 kl. 00:17 skrev Hoopes, Andrew :
>
> Hi Julia,
>
> This is a small bug that's been fixed in the 7.1.1 patch release. I would
recommend updating freesurfer versions (there will be no differences in
recon-all results).
>
> Best,
> A
Hi James,
It sounds like your target filesystem does not support symlinks? The answer to
your question depends on how you are actually copying data, and you should
probably contact your IT about this, but if you’re using rsync to move recons,
you can supply the --copy-links flag to transform sy
Your best bet is using the FS matlab library to script annotation edits (see
read_annotation.m and write_annotation.m). Otherwise, if you’re using
freesurfer 6, you can use tksurfer to manually edit labels/annotations through
the GUI (https://surfer.nmr.mgh.harvard.edu/fswiki/tksurfer_labeledit)
Hi Julia,
This is a small bug that's been fixed in the 7.1.1 patch release. I would
recommend updating freesurfer versions (there will be no differences in
recon-all results).
Best,
Andrew
On 10/13/20, 8:44 AM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of
Julia Lam" wrote:
You can’t open an annotation as a plain text file – it’s a custom binary
structure. You can visualize it on top of a surface in freeview. Something like:
freeview -f surf/lh.inflated:annot=label/lh.aparc.annot
From: on behalf of 1248742467
<1248742...@qq.com>
Reply-To: FS Help
Date: Tuesday, O
Hi Michele,
Does $FREESURFER_HOME/mni/bin/nu_correct exist for you? This error usually
indicates that you have not configured the freesurfer environment correctly.
Have you sourced the SetUpFreeSurfer script?
Best,
Andrew
From: on behalf of Michele Valotti
Reply-To: FS Help
Date: Wednesday
Hi James, please ignore that step. In fact, adding those matlab paths to your
default DYLD_LIBRARY_PATH will most likely mess up freesurfer binaries in your
environment.
Andrew
From: James Hartzell
Date: Tuesday, September 22, 2020 at 2:19 PM
To: "Hoopes, Andrew"
Cc: FS Help
S
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