Freesurfer

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30070 discussions

Requesting pass code for Ubuntu 18.04.06 compressed image with the FreeSurfer 7.2.0
by Adam Tartaglia 21 Nov '22

21 Nov '22

External Email - Use Caution Hello, Can I get the pass code for the Ubuntu 18.04.06 compressed image with the FreeSurfer 7.2.0 release installed on it? Thank you, - Adam

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Passcode for Freesurfer 7.2.0
by Adam Tartaglia 21 Nov '22

21 Nov '22

External Email - Use Caution Good morning, Would you please send me the pass code for opening the archive of FS 7.2.0? Thank you, - Adam

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Re: [Freesurfer] aparcstats2table segmentation fault error
by fsbuild 20 Nov '22

20 Nov '22

External Email - Use Caution You don’t need to manually set MINC_BIN_DIR or the MINC_LIB_DIR variables as those should get set when you source the freesurfer setup script. Try manually running the bash shell, set FREESURFER_HOME, and check you can see that directory, $ bash$ export FREESURFER_HOME=/home/ericlyn/local/easybuild/software/2020/Core/freesurfer/7.2.0$ ls $FREESURFER_HOME< … output deleted but you should see the top of the tree including the SetUpFreeSurfer.sh script you are going to source … > Then source the setup script, $ source $FREESURFER_HOME/SetUpFreeSurfer.sh< … output deleted … > Then try running the command in debug mode and see if you get the help output.  If you see the help output, then the command ran. $ bash -x `which aparcstats2table` --help + '[' '!' -e  /home/ericlyn/local/easybuild/software/2020/Core/freesurfer/7.2.0']'+ exec /homes/1/rd521/freesurfer/dev/bin/fspython /homes/1/rd521/freesurfer/dev/python/scripts/aparcstats2table —help< … help output deleted ... > - R. On Nov 15, 2022, at 22:07, fsbuild <fsbuild(a)contbay.com> wrote:        External Email - Use Caution        Difficult to enlarge your screenshots and read the text, but it looks like even though the output from the setup script displays the path to FREESSURFER_HOME, the script wrapper for the shell cannot verify that path actually exists.   And it looks like you are using a “dot” directory named “.local” in your path for FREESURFER_HOME which is usually reserved for hidden subdirs in the shell.  I would not name any subdirectory to begin with a "dot" for normal use with the shell, so try$ mv .local local… reset FREESURFER_HOME, source the setup script again, and see if running the command works.- R.On Nov 15, 2022, at 19:59, Eric Yin <eric.yin(a)mail.utoronto.ca> wrote:        External Email - Use Caution        Hello! I’m trying to run the aparcstats2table function on a single participant and I cannot seem to get rid of the following segmentation fault error. I checked the forums and did not find anyone with the same problem. <9ECE8F5D2E7645A5962B55E842687C47.png> I have tried a few different options. First, I read that aparcstats2table requires PATH to lead to python2, but this call would throw the error that freesurfer has not been sourced properly even though I sourced it manually. Please find my Freesurfer version in the screenshot as well. I’m running on CentOS Linux v7 (Core). <4E289904EB384B21861CA9E16B7DD234.png> Then I thought that it might be because freesurfer/7.2.0 requires a newer version of python, but it also did not work for python3 or python3.6. <64B17BE84D1E4AFBBF7FFCE28ED15CD7.png> Please let me know if I’m doing something wrong, or if anyone has run into a similar issue. Thank you for your time._______________________________________________Freesurfer mailing listFreesurfer(a)nmr.mgh.harvard.eduMailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1FgpEnfiQUT43jn39cU5NylGOXNr2K7trxyVjQ… mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Re: [Freesurfer] aparcstats2table segmentation fault error
by fsbuild 20 Nov '22

20 Nov '22

External Email - Use Caution Difficult to enlarge your screenshots and read the text, but it looks like even though the output from the setup script displays the path to FREESSURFER_HOME, the script wrapper for the shell cannot verify that path actually exists.   And it looks like you are using a “dot” directory named “.local” in your path for FREESURFER_HOME which is usually reserved for hidden subdirs in the shell.  I would not name any subdirectory to begin with a "dot" for normal use with the shell, so try $ mv .local local … reset FREESURFER_HOME, source the setup script again, and see if running the command works. - R. On Nov 15, 2022, at 19:59, Eric Yin <eric.yin(a)mail.utoronto.ca> wrote:        External Email - Use Caution        Hello! I’m trying to run the aparcstats2table function on a single participant and I cannot seem to get rid of the following segmentation fault error. I checked the forums and did not find anyone with the same problem. <9ECE8F5D2E7645A5962B55E842687C47.png> I have tried a few different options. First, I read that aparcstats2table requires PATH to lead to python2, but this call would throw the error that freesurfer has not been sourced properly even though I sourced it manually. Please find my Freesurfer version in the screenshot as well. I’m running on CentOS Linux v7 (Core). <4E289904EB384B21861CA9E16B7DD234.png> Then I thought that it might be because freesurfer/7.2.0 requires a newer version of python, but it also did not work for python3 or python3.6. <64B17BE84D1E4AFBBF7FFCE28ED15CD7..png> Please let me know if I’m doing something wrong, or if anyone has run into a similar issue. Thank you for your time._______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Pass code for archive "FS_7_2_0_Ubuntu_18_04_06.ova.7z"
by Диляра Айнуллова 20 Nov '22

20 Nov '22

External Email - Use Caution Hello! My name is Dilyara. I’m student of Kazan State Medical University and I’d like to use your programm for my science work. At this guide https://secure-web.cisco.com/1GwjFRQ-2FvgOFd6Y8S6_UDcGBJRfOPG2YVvMfZxJnTB3r… I saw lines "If you do not have the pass code to open the image, then send an email to the FreeSurfer help list to receive it." May I ask you to send me pass code for archive "FS_7_2_0_Ubuntu_18_04_06.ova.7z" -- Dilyara Aynullova Отправлено из Почты Mail.ru

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FS 7.2 Ubuntu pass required
by Tabasi, Farhad 18 Nov '22

18 Nov '22

External Email - Use Caution Hello, I am installing the Virtual Machine to run Freesurfer, and I prompted with a password. Could you please share the password with me? Thank you for your help. Regards, Farhad Tabasi

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Supplying a mask to recon-all?
by Xinyu Liu 18 Nov '22

18 Nov '22

External Email - Use Caution Dear experts, I am trying to use freesurfer with a set of high-resolution images (0.6mm3 isotropic) and I found the brain mask generated by freesurfer is not ideal. In this case, is it possible to supply a mask to recon-all? I've seen in previous communications it has been suggested to run auto-recon1, replace the mask and proceed with auto-recon2 etc, but I was hoping to use recon-all directly if that's possible. Or is it possible to run recon-all with skull-stripped image? Thank you very much. Best Xinyu

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Passcode request
by emma.sophie＠gmx.net 18 Nov '22

18 Nov '22

External Email - Use Caution Dear Sir or Madam, I would like to request the passcode for the FS_7_2_0_ubuntu_18_04_06.ova.7z file. I can`t open it without one. Thank you very much for your help. Yours sincerely, Emma Wiedenmann

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Fwd: Longitudinal FS pipeline consistently interrupts at -Sphere for all participants
by Julie Ottoy 17 Nov '22

17 Nov '22

External Email - Use Caution Hi FS team, Just wanted to follow up with my question below. Thanks! Julie ---------- Forwarded message --------- From: Julie Ottoy <julie.jj.ottoy(a)gmail.com> Date: Fri, 4 Nov 2022 at 00:11 Subject: Re: [Freesurfer] Longitudinal FS pipeline consistently interrupts at -Sphere for all participants To: fsbuild <fsbuild(a)contbay.com> Hi Fsbuild team, Thank you for your reply. Sorry for the confusion, my system was actually Linux, not Windows. It did *not* run on top of Windows (sorry again for the confusion). In any case, I tried both the longitudinal pipeline FS v7.1.1 and v7.2 consistently on Linux. I also used two different machines (our institute server as well as ComputeCanada, hence I do not believe it's a memory issue). Each run got stuck at the -Sphere x.long.x step as indicated in my previous email. Interestingly, I tried today with the longitudinal FS v6.0.0 (kept all the rest the same) and it ran fine! Could there be any bug in the v7 series for longitudinal processing that was not present in the v6 series? I tried on two different types of input T1w data acquired from different centers and they point to the same issue => -Sphere error in x.long.x for v7 , while it runs fine for v6. Please see attached log files and screenshots for both. I am also thinking if it would be ok to run the longitudinal with v6 since we ran the baseline data with v7.2. Could you please advise on this? Last, I was wondering if there is a way to receive more detailed log/error files? As indicated from my previous email and screenshots, the code just exited at Sphere but did not indicate why it went wrong there. Thank you for your help! Best regards Julie On Wed, 2 Nov 2022 at 17:02, fsbuild <fsbuild(a)contbay.com> wrote: > One way we’ve seen recon-all eventually fail running on Linux hosted on > Windows is whatever is virtualizing Linux to run on top of the Windows OS - > simply runs out of memory at some point in the processing pipeline. That > can result in a message in the recon-all.log like a file was not found, > i.e., a computation fails and the results are not saved in a file that > later on is expected to be found, opened and read. I don’t see messages > like that in your log. > > It might be helpful to know more about how you are running Linux on > windows, e.g., if you are using the built-in Windows Subsystem for Linux > (WSL) or using a VM running on something like VirtualBox. > > You could also send along the output in the linux terminal from: > $ cat /etc/os-release > $ cat $FREESURFER_HOME/build-stamp.txt > > - R. > > On Nov 2, 2022, at 15:03, Julie Ottoy <julie.jj.ottoy(a)gmail.com> wrote: > > <recon-all.log> > > >

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Medial wall mask for FSL tractography
by Renew Andrade 17 Nov '22

17 Nov '22

External Email - Use Caution Dear experts: I have a doubt about finding the medial wall mask of a subject. Would this be ok? mri_label2label --srclabel lh.cortex.label --trglabel lh.cortex.label --outmask lh.cortex.mask.nii.gz --regmethod surface --hemi lh --srcsubject 25633 --trgsubject 25633 fscalc lh.cortex.mask.mgz not -o lh.medialwall.mask.mgz mri_convert lh.medialwall.mask.mgz lh.medialwall.mask.gii If I use mris_decimate to downsample the surface does it change anything of previous and how should I proceed in that case to change it? Best, Rene Andrade.

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