Hello Jacky,

You can try the procedure listed below, which was posted to the list around Dec. 12th. It might work for 7.3.1 release, though I have only tried it on the 7.3.2 release. If it does not work for you on 7.3.1, then I would download and install 7.3.2.

- R.

- - - - - -

If you are running the Freesurfer 7.3.2 release on an Apple Silicon machine (M1/M2 processor) with MacOS BigSur (11.X) or Monterey (12.X) AND have seen the error message "illegal hardware instruction", then please read following..

The "illegal hardware instruction" error can occur when running commands such as samseg and mri_synthseg. This update is not necessary if your normal workflow does not include commands that produce this error.

Please note the update should not be applied if:
- Your Mac has an Intel processor.
- Your Apple silicon machine (M1/M2 processor) is running a version of Freesurfer that is not the 7.3.2 release, e.g., a more recent development build.

UPDATE PROCEDURE:

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 be https://drive.google.com/file/d/15Qeve5FIA137KON67ehKIOyXy1N0PbAC/view?usp=share_link

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.

On Jan 20, 2023, at 05:16, Jacky Lee <cylee10@gmail.com> wrote:

External Email - Use Caution

Hi FreeSurfer developers,

I was trying to do lesion segmentation and calculation with FreeSurfer samseg function on my MS subjects as described here: MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://surfer..nmr.mgh.harvard.edu/fswiki/Samseg

I have performed coregistration and reformatting of my FLAIR image. I proceeded to run_samseg as follows: run_samseg --input 105_t1.nii 105_flairRegT1.nii --pallidum-separate --lesion --lesion-mask-pattern 0 1 --output samsegoutput

Then I encountered this error: zsh: illegal hardware instruction run_samseg --input 105_t1.nii 105_flairRegT1.nii --pallidum-separate --lesion

1) FreeSurfer version: freesurfer-darwin-macOS-7.3..1-20220723-115e466
2) Platform: macOS Ventura 13.1 (22c65) [Apple M1 macbook pro]

Please help looking into it. Thanks

Jacky

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