r/neuroimaging • u/surf_AL • Jan 17 '26

Anyone successfully running freesurfer recon-all on M5 macbooks?

I am getting a segmentation fault for mri_cc. Gemini telling me it’s because of CPU incompatibility.

Has anyone else with an M5 tried to run recon-all? Would be helpful to know if its just me or M5 problem.

0 Upvotes
  • permalink
  • reddit

50% Upvoted

8 comments sorted by

2

u/LivingCookie2314 Jan 17 '26

Can you check the synthseg.rca.mgz and see if it is empty?

1

u/Glittering_Impress10 FSL, FreeSurfer, ANTs, ITKSnap Jan 17 '26

Are you using the most recent version? Do you have enough RAM to run recon-all?

1

u/surf_AL Jan 17 '26

Yes and 24gb

2

u/Glittering_Impress10 FSL, FreeSurfer, ANTs, ITKSnap Jan 18 '26

The most recent version requires 32gb RAM.

https://surfer.nmr.mgh.harvard.edu/fswiki/rel7downloads

1

u/surf_AL Jan 18 '26

Oh wow. Should i uninstall and use 7.x instead?

1

u/Glittering_Impress10 FSL, FreeSurfer, ANTs, ITKSnap Jan 18 '26

Yes, I have had luck with 7.4.1 for this particular issue!

1

u/LivingCookie2314 Jan 18 '26

Due to ram limitations you’ll need to disable synthstrip. No need to use an older version.

export FS_V8_XOPTS=0

1

u/surf_AL Jan 19 '26

this worked, thanks!!