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, https://secure-web.cisco.com/1klszb-du72zzOU81o6pWn28vjYMVSQcTmDSQ_1LxajxX2L...
2) Check the download is OK with the md5 command in the terminal window,
$ md5 tensorflow-2.4.1-py3-none-any.whl MD5 (tensorflow-2.4.1-py3-none-any.whl) = fab44de8702faf65e17a22d706a525a4
DO 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/fspython
4) 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-2.4.1
5) 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-2.4.1
CHECK 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@nmr.mgh.harvard.edu on behalf of Iglesias Gonzalez, Juan E. JIGLESIASGONZALEZ@mgh.harvard.edu Date: Tuesday, 26 September 2023 at 17:35 To: 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 Iglesias http://secure-web.cisco.com/1Gpz43kiNknL9BKam5I7Djq85LOKVEn0-BDgYtOhgMCQJHui...
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Conrad, Julian Julian.Conrad@medma.uni-heidelberg.de Date: Tuesday, September 26, 2023 at 4:38 PM To: 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.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