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Dear Freesurfer Developers,

First of all, thank you for the fantastic work on the Histo Atlas Segmentation tool and the amazing updates in FreeSurfer 8!

Since I encountered some crashes with mri_histo_atlas_segment_fireants and mri_histo_atlas_segment_fast, I wanted to share the issues I experienced.

I downloaded FreeSurfer 8 to my M1 MacBook Pro using the installation package, but it partially contains an older code version compared to the one on GitHub for the NextBrain segmentation with FireAnts. For example, it attempts to import FireAnts packages that are not included, such as GreedyRegistration from fireants.registration. I then installed FreeSurfer 8 directly from GitHub, which worked. However, as soon as EasyReg started, I encountered a thread lock. This also occurred when trying to run the EasyReg step directly as a terminal command.

After that, I attempted the installation on Linux. However, in the latest installation package for Ubuntu 18, the ERC_bayesian_segmentation folder was completely missing. I then installed it again directly from GitHub but ran into a similar issue with EasyReg during the mri_histo_atlas_segment_fireants process, even when using only a single thread.

I also tried mri_histo_atlas_segment_fast because my data is 1mm isotropic. However, this also did not work, as it failed when starting the registration with SynthMorph. I was able to resolve this by using the spawn method for multiprocessing, preventing issues when processing both hemispheres simultaneously.

Additionally, I noticed that mri_TumorSynth is missing, although it is listed on the FreeSurfer wiki page. I hope it will be available in an updated version of FreeSurfer 8.

Thanks in advance!

Best regards,

Lukas von Erdmannsdorff