Freesurfer September 2023

freesurfer@nmr.mgh.harvard.edu

71 participants
88 discussions

Re: [Freesurfer] Recon-all-clinical error: Illegal instruction Error in SynthSeg
by fsbuild 26 Sep '23

26 Sep '23

External Email - Use Caution  Besides patching the python distribution, another option available now is the development arm64 build for silicon Macs with an M1, M2 processor.  But this is not a release build and so has not been tested like a stable release.  The dev builds are currently ~3 months post the 7.4.1 release from back in June of this. year.  We’d be happy to hear how it goes if you try it.  The download links are below. - R.https://secure-web.cisco.com/1aFiKh6YzbcJ_9V-mQth29TZB1SeCRdpmUdrLhAH6aMS… https://secure-web.cisco.com/1M-Y1AHK0ybK-HgTbS6EGioPOtjnLKD9oxxiz5O9fG-v6v… On Sep 26, 2023, at 18:01, Sorby-Adams, Annabel <ASORBY-ADAMS(a)mgh.harvard.edu> wrote:        External Email - Use Caution        Hi Julian, I have managed to run recon-all on my Apple M1 macOS Ventura using the 7.3.2 version of Freesurfer. It does not work on 7.4.2 or dev versions, however. These instructions were posted in a previous correspondence from fsbuild, but reposting here for anyone else having the same issue:  You may not be able to run these commands without sudo/admin permissions on your machine.1) Download the tensorflow-2.4.1-py3-none-any.whl from,MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to behttps://drive.google.com/file/d/15Qeve5FIA137KON67ehKIOyXy1N0PbAC/view?us…) Check the download is OK with the md5 command in the terminal window,$ md5 tensorflow-2.4.1-py3-none-any.whlMD5 (tensorflow-2.4.1-py3-none-any.whl) = fab44de8702faf65e17a22d706a525a4DO NOT PROCEED UNTIL YOU GET THE ABOVE OUTPUT FROM the md5 command.3) Setup the Freesurfer 7.3.2 environment (shown here as installed via .pkg file under /Applications) and verify the path to fspython is from the 7.3.2 release,$ export FREESURFER_HOME=/Applications/freesurfer/7.3.2$ source $FREESURFER_HOME/SetUpFreeSurfer.sh-------- freesurfer-darwin-macOS-7.3.2-20220803-878457d --------... environment variable settings output ...$ which fspython/Applications/freesurfer/7.3.2/bin/fspython4) Uninstall the existing tensorflow package with,$ sudo $FREESURFER_HOME/python/bin/python3 -m pip uninstall tensorflow... apart from any warnings you should see the output ...Successfully uninstalled tensorflow-2.4.15) Install the package downloaded above.  This command assumes the package is in the current directory where the command is run.$ sudo -H $FREESURFER_HOME/python/bin/python3 -m pip install ./tensorflow-2.4.1-py3-none-any.whl... apart from warnings and output about requirements (which should all be satisfied) ...... you should see tensorflow was updated ....Successfully installed tensorflow-2.4.1CHECK THE UPDATE:$ which fspython/Applications/freesurfer/7.3.2/bin/fspython$ fspython>>> import sys, os>>> import tensorflow>>>You should see the prompt return to ">>>" after the import of tensorflow with no errors reported.  Hit Ctrl-D to escape the python session.  The update should now be complete. Once you have done this you should be able to run recon-all via 7.3.2. Hope this works!Annabel From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of Iglesias Gonzalez, Juan E. <JIGLESIASGONZALEZ@mgh.harvard.edu>Date: Tuesday, 26 September 2023 at 17:35To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>Subject: Re: [Freesurfer] Recon-all-clinical error: Illegal instruction Error in SynthSeg        External Email - Use Caution        Dear Julian,I believe this is a problem with SynthSeg not being compatible with the new microprocessor in MAC computers. Our software engineers are looking into solutions to this.Sorry for the inconvenience,Eugenio --Juan Eugenio Iglesiashttp://http://secure-web.cisco.com/1DgebDH1WCLKceFhMcyIutLihRRkTXmu… <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of Conrad, Julian <Julian.Conrad@medma.uni-heidelberg.de>Date: Tuesday, September 26, 2023 at 4:38 PMTo: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>Subject: [Freesurfer] Recon-all-clinical error: Illegal instruction Error in SynthSeg        External Email - Use Caution        Hello FreeSurfer Developers, I'm attempting to  do a surface reconstruction from a GRE magnitude image using recon-all-clinical.shWhen I am running the pipeline, I get the following error: Illegal instructionError in SynthSeg neuroadmin@medma0236 ~ % recon-all-clinical.sh /Users/neuroadmin/Daten/UMM/ALS/Nifti/RC026_sub-010/ses-mri01/anat/RC026_sub-10_ses-mri01_part-mag.nii RC026_sub-010_ses-mri01 8 /Users/neuroadmin/Daten/UMM/ALS/Nifti/RC026_sub-010/ses-mri01/anat/freesurfer#--------------------------------------------#@# recon-all-clinical Di 26 Sep 2023 21:53:31 CEST mri_convert /Users/neuroadmin/Daten/UMM/ALS/Nifti/RC026_sub-010/ses-mri01/anat/RC026_sub-10_ses-mri01_part-mag.nii /Users/neuroadmin/Daten/UMM/ALS/Nifti/RC026_sub-010/ses-mri01/anat/freesurfer/RC026_sub-010_ses-mri01/mri/native.mgz reading from /Users/neuroadmin/Daten/UMM/ALS/Nifti/RC026_sub-010/ses-mri01/anat/RC026_sub-10_ses-mri01_part-mag.nii...TR=49.00, TE=0.00, TI=0.00, flip angle=0.00i_ras = (0.997386, 0.00125151, 0.0722456)j_ras = (2.37011e-10, 0.99985, -0.0173204)k_ras = (-0.0722564, 0.0172751, 0.997236)writing to /Users/neuroadmin/Daten/UMM/ALS/Nifti/RC026_sub-010/ses-mri01/anat/freesurfer/RC026_sub-010_ses-mri01/mri/native.mgz... Illegal instruction Error in SynthSeg 1) FreeSurfer version: freesurfer-macOS-darwin_x86_64-7.4.12) Platform: MacOS X Darwin Hope this information is sufficient and there is an easy solution.Best regards,Julian _______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Running MATLAB on a MAC PRO
by Alan Francis 26 Sep '23

26 Sep '23

External Email - Use Caution Hi All : I just bought a 2023 MAC PRO with an M2 Ultra Chip for my lab. It's running macOS Ventura. I have installed MATLAB on it but it refuses to run in a terminal or from the Applications folder. MATLAB runs perfectly fine on my other Linux machines. The MATLAB website has very little, if outdated, help. Have any of you encountered this problem? Thanks, Alan -- *|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|* *Alan N. Francis PhDAssistant Professor of NeuroscienceInstitute of Neuroscience* *University of Texas, School of Medicine* *Rio Grande Valley* *Texas.*

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Recon-all-clinical error: Illegal instruction Error in SynthSeg
by Conrad, Julian 26 Sep '23

26 Sep '23

External Email - Use Caution Hello FreeSurfer Developers, I'm attempting to do a surface reconstruction from a GRE magnitude image using recon-all-clinical.sh When I am running the pipeline, I get the following error: Illegal instruction Error in SynthSeg neuroadmin@medma0236 ~ % recon-all-clinical.sh /Users/neuroadmin/Daten/UMM/ALS/Nifti/RC026_sub-010/ses-mri01/anat/RC026_sub-10_ses-mri01_part-mag.nii RC026_sub-010_ses-mri01 8 /Users/neuroadmin/Daten/UMM/ALS/Nifti/RC026_sub-010/ses-mri01/anat/freesurfer #-------------------------------------------- #@# recon-all-clinical Di 26 Sep 2023 21:53:31 CEST mri_convert /Users/neuroadmin/Daten/UMM/ALS/Nifti/RC026_sub-010/ses-mri01/anat/RC026_sub-10_ses-mri01_part-mag.nii /Users/neuroadmin/Daten/UMM/ALS/Nifti/RC026_sub-010/ses-mri01/anat/freesurfer/RC026_sub-010_ses-mri01/mri/native.mgz reading from /Users/neuroadmin/Daten/UMM/ALS/Nifti/RC026_sub-010/ses-mri01/anat/RC026_sub-10_ses-mri01_part-mag.nii... TR=49.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (0.997386, 0.00125151, 0.0722456) j_ras = (2.37011e-10, 0.99985, -0.0173204) k_ras = (-0.0722564, 0.0172751, 0.997236) writing to /Users/neuroadmin/Daten/UMM/ALS/Nifti/RC026_sub-010/ses-mri01/anat/freesurfer/RC026_sub-010_ses-mri01/mri/native.mgz... Illegal instruction Error in SynthSeg 1) FreeSurfer version: freesurfer-macOS-darwin_x86_64-7.4.1 2) Platform: MacOS X Darwin Hope this information is sufficient and there is an easy solution. Best regards, Julian

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Potential bias in the base template
by Maksim Slivka 26 Sep '23

26 Sep '23

External Email - Use Caution Hi FreeSurfer Community, I plan to use longitudinal FreeSurfer to process a set of longitudinal scans that are likely to create a bias in the base template. Specifically, our study consists of 3 scans acquired within the first 20 weeks and a subsequent scan acquired 2 years after the third scan. >From the original publication on longitudinal FreeSurfer, I understand that the longitudinal scans are treated equally and do not require to be evenly distributed in time, and that the cross and base images are only used to initialize the longitudinal processing. However, my concern is that the resulting template, based on the median, will be too similar to the first three scans. Would this negatively impact the results of the 4th scan, due to the inherent bias of the template? Has any group investigated this before? Any feedback would be appreciated! Best regards, Maksim

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-bigventricles
by Taylor, Lisa 25 Sep '23

25 Sep '23

External Email - Use Caution Hi, I'd like to confirm that the flag -bigventricles is a current flag that can be used in version 7.2.0? I see the wiki updates but wanted to make sure the flag works with this version as well as the 6.0 Thank you! Lisa

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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  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(a)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@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 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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Freesurfer September 2023