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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.
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On Sep 26, 2023, at 18:01, Sorby-Adams, Annabel <ASORBY-ADAMS@mgh.harvard.edu> wrote:

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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,
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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

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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://www.jeiglesias.com
 

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

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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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