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Maybe you could let us know the details about what version of MacOS you are running, how much memory your machine has and what the M1 processor has for efficiency and performance cores. - R. On Jun 8, 2025, at 21:25, Treeby, Bradley <b.treeby@ucl.ac.uk> wrote: External Email - Use Caution
Dear FreeSurfer Developers and Community,
I am trying to run Bayesian Segmentation with the Histological Atlas "NextBrain" in FreeSurfer on an M1 Mac on the CPU. I downloaded the 8.0.0 installer and followed the instructions, downloaded the atlas, etc.
If I run mri_histo_atlas_segment_fast. It runs until “Reading in atlas” and then fails with a long error trace including "An attempt has been made to start a new process before the current process has finished its bootstrapping phase."
If I run mri_histo_atlas_segment_fireants it quits almost immediately, complaining about missing modules (‘fireants.registration.deformation.geodesic’).
My call in both cases follows:
mri_histo_atlas_segment_xxx $SUBJECT_IM $SUBJECTS_DIR/$SUBJECT_ID/mri_histo_atlas_seg/ 0 $FS_THREADS
Are there any pointers, or some setup steps that I’ve missed? If it’s helpful, other tools like recon-all are working correctly. I’m excited to try this out!
Best,
Bradley Treeby. _______________________________________________ Freesurfer mailing list -- freesurfer@nmr.mgh.harvard.edu To unsubscribe send an email to freesurfer-leave@nmr.mgh.harvard.edu https://secure-web.cisco.com/1LRJFj-q1whe_aJdjQvnpHmOonFsjyU1a_OJFlT1gMirGbr...
External Email - Use Caution
Thanks so much for the quick reply.
I mis-spoke, it’s actually an M3 mac. Details are: - Chip Apple M3 Pro (12 cores, 6 performance and 6 efficiency) - Memory 36 GB - macOS Sequoia 15.5
I’ve tried running xx_fast with 1, 4, and 8 threads and get the same failure.
Best, Brad.
On 9 Jun 2025, at 11:11, fsbuild fsbuild@contbay.com wrote:
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External Email - Use Caution
Maybe you could let us know the details about what version of MacOS you are running, how much memory your machine has and what the M1 processor has for efficiency and performance cores.
- R.
On Jun 8, 2025, at 21:25, Treeby, Bradley b.treeby@ucl.ac.uk wrote:
External Email - Use Caution
Dear FreeSurfer Developers and Community,
I am trying to run Bayesian Segmentation with the Histological Atlas "NextBrain" in FreeSurfer on an M1 Mac on the CPU. I downloaded the 8.0.0 installer and followed the instructions, downloaded the atlas, etc.
If I run mri_histo_atlas_segment_fast. It runs until “Reading in atlas” and then fails with a long error trace including "An attempt has been made to start a new process before the current process has finished its bootstrapping phase."
If I run mri_histo_atlas_segment_fireants it quits almost immediately, complaining about missing modules (‘fireants.registration.deformation.geodesic’).
My call in both cases follows:
mri_histo_atlas_segment_xxx $SUBJECT_IM $SUBJECTS_DIR/$SUBJECT_ID/mri_histo_atlas_seg/ 0 $FS_THREADS
Are there any pointers, or some setup steps that I’ve missed? If it’s helpful, other tools like recon-all are working correctly. I’m excited to try this out!
Best,
Bradley Treeby. _______________________________________________ Freesurfer mailing list -- freesurfer@nmr.mgh.harvard.edu To unsubscribe send an email to freesurfer-leave@nmr.mgh.harvard.edu https://secure-web.cisco.com/17XF9tP5-VJCG58LQGFiQCnclxUI2LrxVnCdSZR2IRwThxA...
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Treeby, Bradley