I am attempting to use Freesurfer on MacOS Ventura (version 13.5.2) with an M2 Pro silicone chip and GPU. I have successfully installed Freesurfer version 7.4.1.

I am trying to use samseg for cross-sectional MS lesion volume analysis by running the following command:

run_samseg --input Freesurfer_subjects/T1.nii Freesurfer_subjects/FAMUS/T2FLAIR_reg.nii --pallidum-separate --lesion --lesion-mask-pattern 0 1 --output Freesurfer_subjects/FAMUS/samseg

I get the error message:

zsh: illegal hardware instruction  run_samseg --input Freesurfer_subjects/FAMUS/T1.nii   --lesion  0 1

 

As described in the samseg manual, one may be prompted to use Tensorflow when using this module for the first time. I was not prompted to do so but I did install it (and python3 as well) using the instructions here: MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://www.tensorflow.org/install/pip

After this, I still get the above error message.

I can also see that there is no support for running Tensorflow on Mac with GPU.

Does this mean that there's no way for me to run this command or is there anything else I can try to solve this?

Of note, the basic samseg command (run_samseg --input <file> [<file> ...] --output <dir> [--threads <threads>] [--pallidum-separate]) is running without any issues.

Thank you,

Bianka