Freesurfer

freesurfer@nmr.mgh.harvard.edu

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Re: [Freesurfer] Unable to complete all the steps of recon-all
by fsbuild 25 Sep '23

25 Sep '23

External Email - Use Caution  If the files can be read from inside the VM from the external drive, then I'd think you could copy them into the Linux file system.  You would have to run the “mount” or some other command in the Linux terminal window to determine the path on the exFAT drive to what SUBEJCTS_DIR is there.  But usually things are mounted under /media $ mount | grep media… check output ... Let’s say your path to SUBJECTS_DIR on the exFAT drive as visible in the Linux file system is /media/exfat/data/subj034 You need to find a location in Linux where you have enough space to copy the data.  I will assume using your home directory in the Linux VM below.  So in the Linux terminal window to use your home directory you could try the commands below.   NOTE - that if you have spaces in a path or directory name on the exFAT drive, then quote them below, e.g.,  subj 034  ==>  "subj 034" $ cd… or ...$ cd $HOME$ pwd/home/developer     <— your result will differ… see how much disk space you have …$ df -h .… check output … and if you have enough space to copy data, if so, make a subdirectory for the copy …$ mkdir data_copy$ cd data_copy… try using the tar utility to copy all data from the drive …$ (cd /media/exfat/data; tar cpf - subj034) | tar xpf -… may take a while depending on speed of drive and size of data … $ cd subj034… check all the data is there $ ls -lRt * | more… hit q to stop output from more command ... $ pwd/home/developer/data_copy/subj034 … then set SUBJECTS_DIR in the environment or in script, etc. that runs the recon-all $ export SUBJECTS_DIR=/home/developer/data_copy/subj034 - R. On Sep 25, 2023, at 02:52, Mervin Tee <mervintee(a)nus.edu.sg> wrote:        External Email - Use Caution        Hi R,Thanks for getting back, indeed a copy of those files doesn't help because just like what you have mentioned at some point a check failed and I could not proceed with the remaining steps of recon-all. The command I pasted was obtain from the last line of the error log text file where it indicates where the step of which the error occurred. But the main error is mostly due to symlink on exFAT storage on linux. Hence, the question here is if there is any solution that allows me to still work on external exFAT storage. As symlink doesn't seems to work on exFAT storage. As my data are bitlocked on an external storage, which doesn't allow me to change the format for the storage drive. So, I was hoping to look for a workaround that allows me to continue working on exFAT storage.  Cheers,Mervin From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of fsbuild <fsbuild@contbay.com>Sent: 25 September 2023 10:10To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>Cc: Mervin Tee <mervintee@nus.edu.sg>Subject: Re: [Freesurfer] Unable to complete all the steps of recon-all  - External Email -         External Email - Use Caution         I don’t see an error message in  what you posted below.I would not assume changing soft links to actual copies of the same file (by a different name) will work, i.e., anything that makes a soft link may subsequently test for a soft link using the link name.  That test will fail if the soft link has been replaced by an actual (duplicate) copy of the file.  The expectation is when writing output e.g., during recon-all, that SUBJECTS_DIR points to a linux compatible file system that supports creating all the Linux file system file types (including soft links) and support all Linux file privileges.-R.On Sep 24, 2023, at 01:58, Mervin Tee <mervintee@nus.edu..sg> wrote:        External Email - Use Caution        Hi, I'm trying to complete my recon-all command. I'm currently working on Ubuntu 22 and processing the images from an exFAT drive.After digging a bit, I realised that symbolic links cannot be created on exFAT drives. I then came across another post that suggest to change all 'ln' to cp instead. While that works for the remaining steps. It started exiting with errors at this stage..The stage where it stops#@# Qdec Cache preproc lh white.K fsaverage Wed Sep 13 15:40:33 +08 2023The error that was in the error log.CMD mris_preproc --s ED751_SAG_MPRAGE_p2_NON-SSc.nii --hemi lh --meas white.K --target fsaverage --out lh.white.K.fsaverage.mghWhat should I do to resolve this issue? Cheers,Mervin Important: This email is confidential and may be privileged. If you are not the intended recipient, please delete it and notify us immediately; you should not copy or use it for any purpose, nor disclose its contents to any other person. Thank you._______________________________________________Freesurfer mailing listFreesurfer(a)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/freesurferImportant: This email is confidential and may be privileged. If you are not the intended recipient, please delete it and notify us immediately; you should not copy or use it for any purpose, nor disclose its contents to any other person. Thank you._______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard..edu/mailman/listinfo/freesurfer

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Re: [Freesurfer] Unable to complete all the steps of recon-all
by Mervin Tee 24 Sep '23

24 Sep '23

External Email - Use Caution Hi, I'm trying to complete my recon-all command. I'm currently working on Ubuntu 22 and processing the images from an exFAT drive. After digging a bit, I realised that symbolic links cannot be created on exFAT drives. I then came across another post that suggest to change all 'ln' to cp instead. While that works for the remaining steps. It started exiting with errors at this stage. The stage where it stops #@# Qdec Cache preproc lh white.K fsaverage Wed Sep 13 15:40:33 +08 2023 The error that was in the error log. CMD mris_preproc --s ED751_SAG_MPRAGE_p2_NON-SSc.nii --hemi lh --meas white.K --target fsaverage --out lh.white.K.fsaverage.mgh What should I do to resolve this issue? Cheers, Mervin ________________________________ Important: This email is confidential and may be privileged. If you are not the intended recipient, please delete it and notify us immediately; you should not copy or use it for any purpose, nor disclose its contents to any other person. Thank you.

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(no subject)
by Michael Mc Laughlin 24 Sep '23

24 Sep '23

External Email - Use Caution Hi, I am curious to know why Freesurfer prefers a T1 weighted scan to a T2 weighted one. Superficially at least, the T2 scan appears to have as good GM/WM contrast with the added benefit of being able to more easily distinguish CSF from bone. [image: image.png] [image: image.png] The above scans are from ERNIE test subject. The first one is T1 weighted and the second is T2 weighted. Michael McLaughlin,

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Native darwin_arm64 development build for silicon Macs
by fsbuild 23 Sep '23

23 Sep '23

External Email - Use Caution  A native silicon Mac build (darwin_arm64) from the freesurfer development branch is currently available for download (along with the usual darwin_x86_64 Intel Mac build).  This means freeview and most binaries should run on current Macs with M1, M2, M3 arm64 processors without using the Rosetta emulation environment required to run Intel binaries.  The build also includes Apple's tensorflow modules for arm64 python. https://secure-web.cisco.com/19iU6Duk2zpbfifexEEBWTZjtW6_df80in56MrW1gz_nnh… https://secure-web.cisco.com/1XTLOzwkVakfd1RBsibgQ7t6YC509CBc7vc-fZFabprKBs… The usual caveat applies if you are contemplating switching from a previous/older freesurfer build or release to a different freesurfer build or release compiled for a different architecture/platform.  We provide this advice at the bottom of the Freesurfer 7.X release page, https://secure-web.cisco.com/1AR0zDCFfQrz2YrY4j9dkUT8euQVsY4AHiC6ltxf0tEGe5… Important Note: When processing a group of subjects for your study, it is essential to process all your subjects with the same version of FreeSurfer, on the same OS platform and vendor, and for safety, even the same version of the OS. While we continue to work to ensure that results match across platforms, there are none-the-less system-level libraries that are OS dependent. An exception to this rule is that you may view and edit files across any platform or version, and run some post-processing tools (outside the recon-all stream) if you check with us first (for instance you may run the longitudinal processing with newer versions). As of this writing, development builds are post the 7.4.1 release from June 2023.  We don't encourage use of dev builds instead of a previous release unless the dev build contains a bug fix or new functionality you need, i.e., dev builds are not expected to be as stable as releases.  That being said, please let us know if you run into issues when trying the new build.   We have not compared the performance of the arm64 binaries against the Intel binaries. - R.

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Follow up question on group analysis (mri_glmfit)
by inbal paran 23 Sep '23

23 Sep '23

External Email - Use Caution Thanks for the quick response. So I followed the steps of the tutorial and performed group analysis by running mris_preproc, then mri_surf2surf and then mri_glmfit. Is that the correct way to do that? and in this case, can I include multiple continuous variables in my analysis (in the fsgd file)? Thanks again Inbal -------- It is worse -- we do not support qdec anymore On 8/5/2023 6:04 AM, inbal paran wrote: External Email - Use Caution Hello FreeSurfer Developers, I have a question regarding group analysis: When I followed the instructions on how to build my FSGD file, it said that:"FSGD files are created automatically by qdec, but qdec is currently (12/9/08) limited to two continuous variables and two discrete variables with two levles. Is this still the case, or is it possible to include more than 2 continuous variables? The freesurfer version I am using: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 Thank you Inbal -- *Inbal Paran, M.PT <http://secure-web.cisco.com/1w6eByVfQtHP57lPYq2r_KIYGKXnqPLFlDOaO0p2X1WZmr0…>.* Schwartz Movement analysis & Rehabilitation Laboratory, Physical Therapy Department, Recanati School for Community Health Professions. Faculty of Health Sciences at Ben-Gurion University of the Negev.

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lta_convert does not produce ITK transforms that are correctly applied by antsApplyTransforms
by Yazdan Rezaee Jouryabi 23 Sep '23

23 Sep '23

External Email - Use Caution Dear all, Hi for checking registration i used fsl applyxfm on an Image(1)(Called Image.nii ) with specific Registration Matrice (Which we suppose to receive when we apply registration Methods) and Generate the "fsl_resampled.nii.gz" (Note: Image Orientations were LAS and in one other Experiment with also the same problem PSR) for our case i will attach the "fsl.mat" (Desired Matrix) using, fsl, freesurfer, and ants i got the correct results (let's call them "fslregistered.mat" and "freesurfer.mat" the converted lta to fsl-liked Matrix) Everything is OK till now But the converted lta-like and fsl-like matrix for ANTs (Which are called ants.lta, and ants.mat) using the lines below: - ConvertTransformFile 3 ./ANTS/ants_0GenericAffine.mat ./ANTS/ants.txt - lta_convert --initk ./ANTS/ants.txt --outlta ./ANTS/ants.lta --src ./Image.nii --trg ./fsl_resampled.nii.gz --ltavox2vox - lta_convert --inlta ./ANTS/ants.lta --outfsl ./ANTS/ants.mat --src ./Image.nii --trg ./fsl_resampled.nii.gz As All Results Images (Registered Image of all Methods) are aligned perfectly i think that there might be some issues with lta_convert Best Regards Yazdan Rezaee J *P.S. *" I've checked the one similar mail one this topic and the conclusion on that was about (sform, qform) incompatibility but the affine matrices of S-form and q-form are equivalent in my case."

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Convert Freesurfer segmentations to OBJ files
by Byripudi Naveen Kumar ed20d402 21 Sep '23

21 Sep '23

External Email - Use Caution Dear experts, I am trying to convert freesurfer segmentations to obj files for visualization in virtual reality. How to do this without losing any segmentation label names and colors. I tried to import the surfaces into 3d slicer but I could not do it. Also can you guide me on how to combine the tractography segments from tracula with the anatomical segmentations from recon-all? Thank you in advance Yours sincerely Naveen Kumar

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Training in Advanced Statistical Methods in Neuroimaging and Genetics, April 15 - 26, 2024
by ROBERT CARY WELSH 20 Sep '23

20 Sep '23

External Email - Use Caution Hi Folks, Our NIH-funded course, “Training in Advanced Statistical Methods in Neuroimaging and Genetics”, will be held in-person in Salt Lake City, UT, from April 15 - 26, 2024. This is a course geared to advanced undergraduate students graduate students, postdocs, and junior faculty. Topics include (see website for more details): Bayesian methods of functional connectivity and activation, longitudinal modeling, network neuroscience, polygenic risk scores, multimodal modeling and predictive modeling. The course is a mix of lectures and hands-on computer labs. Our main lecturers include: Martin Lindquist, Johns Hopkins University Mandy Mejia, Indiana University Rick Betzel, Indiana University Anna Docherty, University of Utah To read more about the course and to apply please see: neurostatsbootcamp.org<http://secure-web.cisco.com/1WGCNO64hrsDRKsP26U8raRZJtaEs4uG-nIYndj55ZcaHIY…> The application (which is multi-part, so please read the detailed instructions) deadline is November 1, 2023. We also offer a limited number of need-based tuition-reduction awards. This is a not-for-profit course and faculty are supported by NIH R25NS117281. Prior testimonials, “This course changed my life”, “I truly learned a lot!”, “This was an excellently planned course.” For more information email us at neurostats(a)g.ucla.edu Best, Robert and Anna ----------- Robert Welsh Professor-in-Residence UCLA Anna Docherty Associate Professor University of Utah

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Re: [Freesurfer] mri_convert: Segmentation fault (core dumped) synthsr scan
by fsbuild 19 Sep '23

19 Sep '23

External Email - Use Caution Hello Ken, The output from your linux shell limits in the log show the following, cputime      unlimitedfilesize     unlimiteddatasize     unlimitedstacksize    8192 kbytescoredumpsize 0 kbytesmemoryuse    unlimitedvmemoryuse   unlimiteddescriptors  1024 memorylocked 64 kbytesmaxproc      7823 maxlocks     unlimitedmaxsignal    7823 maxmessage   819200 maxnice      0 maxrtprio    0 maxrttime    unlimited I would set at least coredumpsize to something non-zero so you can at least get a core file saved that could be looked at.   By default the limits on my Ubuntu 22 system are: $ ulimit -areal-time non-blocking time  (microseconds, -R) unlimitedcore file size              (blocks, -c) unlimiteddata seg size               (kbytes, -d) unlimitedscheduling priority                 (-e) 0file size                   (blocks, -f) unlimitedpending signals                     (-i) 378881max locked memory           (kbytes, -l) 64max memory size             (kbytes, -m) unlimitedopen files                          (-n) 1048576pipe size                (512 bytes, -p) 8POSIX message queues         (bytes, -q) 819200real-time priority                  (-r) 0stack size                  (kbytes, -s) 8192cpu time                   (seconds, -t) unlimitedmax user processes                  (-u) unlimitedvirtual memory              (kbytes, -v) unlimitedfile locks                          (-x) unlimited You can try setting the core file size to unlimited with, $ ulimit -c unlimited... then check the value was changed to something > 0 ...$ ulimit -a You could increase memory size (and as many shell limits as possible) to unlimited to get the max size allowed by the system in the script you use to run recon-all, and then try running recon-all  again to see if you can retrieve a core dump file. - R. On Sep 16, 2023, at 09:55, KennethSPrice <KennethSPrice(a)protonmail.com> wrote:        External Email - Use Caution        OK, I've attached the log file. ------- Original Message -------On Friday, September 15th, 2023 at 2:59 PM, fsbuild <fsbuild(a)contbay.com> wrote:        External Email - Use Caution         It might help if you could send along the crash report as an attachment..-R.On Sep 15, 2023, at 14:36, KennethSPrice <KennethSPrice(a)protonmail.com> wrote:        External Email - Use Caution        Update: I tried running recon-all (5.1, ubuntu 18) on a sample MPRAGE scan and got the "mri_convert: segmentation fault (core dumped)" error again. Any clarity on this issue would be appreciated. Thanks,K------- Original Message -------On Thursday, September 14th, 2023 at 10:41 PM, KennethSPrice <KennethSPrice(a)protonmail.com> wrote:Howdy yall,I ran a subject through synthsr (freesurfer 7.4) and am trying to run the output through the freesurfer 5.1 pipeline (the rest of my dataset was processed with 5.1). I am getting the error "Segmentation fault (core dumped)" during the mri_convert step. Any suggestions? Thanks,Ken_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer<recon-all.log>_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Re: [Freesurfer] freeview upgrade isn’t working/library issue
by fsbuild 19 Sep '23

19 Sep '23

External Email - Use Caution  I don't think we can guarantee upgrading freeview will work with the existing libraries in a sufficiently old freeview distribution.  I’m not sure what version of Ubuntu is running from the kernel listed below, but you could create a backup of your existing freesurfer tree (if you need to keep it), and then run the .deb freesurfer 7.4.1 installer matching your system (Ubuntu 18, 20, 22) which you can download from,  https://secure-web.cisco.com/1W5Z7do8RHfQJIQIHZ9EbWhe5GYVhLQ8shO8lqEwhsAE6g… - R. On Sep 19, 2023, at 15:33, Hoptman, Matthew (NKI) <Matthew.Hoptman(a)nki.rfmh.org> wrote:        External Email - Use Caution        TO: freesurfer@nmr.mgh.harvard.eduFROM: matthew.hoptman@nki.rfmh.orgSUBJECT: freeview upgrade isn’t working/library issue Hello FreeSurfer Developers, I followed the instructions here to upgrade freeview:MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to behttps://surfer.nmr.mgh.harvard.edu/fswiki/UpdateFreeviewI am now getting the error: freeview: error while loading shared libraries: libvtkDomainsChemistry-7.1.so.1: cannot open shared object file: No such file or directory I saw that it was recommended to install the package libvtk7.1, but that isn’t working:E: Unable to locate package libvtk7.1E: Couldn't find any package by glob 'libvtk7.1' Any help is appreciated. I am using:5.4.0-122-generic #138-Ubuntu SMP Wed Jun 22 15:00:31 UTC 2022 x86_64 x86_64 x86_64 GNU/LinuxThanks, Matt  IMPORTANT NOTICE: This e-mail is meant only for the use of the intended recipient. It may contain confidential information which is legally privileged or otherwise protected by law. If you received this e-mail in error or from someone who was not authorized to send it to you, you are strictly prohibited from reviewing, using, disseminating, distributing or copying the e-mail.PLEASE NOTIFY US IMMEDIATELY OF THE ERROR BY RETURN E-MAIL AND DELETE THIS MESSAGE FROM YOUR SYSTEM. Thank you for your cooperation. IMPORTANT NOTICE: This e-mail is meant only for the use of the intended recipient. It may contain confidential information which is legally privileged or otherwise protected by law. If you received this e-mail in error or from someone who was not authorized to send it to you, you are strictly prohibited from reviewing, using, disseminating, distributing or copying the e-mail. PLEASE NOTIFY US IMMEDIATELY OF THE ERROR BY RETURN E-MAIL AND DELETE THIS MESSAGE FROM YOUR SYSTEM. Thank you for your cooperation. _______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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