Thank you for the example files.
I understood that the CAT12 and SimNIBS segmentation processes were not working properly if the .nii files missed both the sform and qform matrices - which is the case of your .nii volume.
I tried to fix this issue with this commit: Bugfix: Running CAT12 and SimNIBS with files without sform/qform · brainstorm-tools/brainstorm3@672f30b · GitHub
Update Brainstorm, then try running again CAT12.
You should see close to the start of the process the message:
BST> Adding default world transformation to MRI...
I haven't executed the entire CAT12 segmentation, so maybe there are other related problems downstream.
Please let me know if this is sufficient to fix the problem.
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Is it possible to open multiple instances of Matlab and then Brainstorm and do the segmentations for multiple subjects in the same database in parallel, or will this corrupt the database somehow?
No, the temporary folder for CAT12 is in your user folder: $HOME/.brainstorm/tmp/cat12.
To execute multiple instances of CAT12 from Brainstorm, you need to run them from different users.
If you are interested in large-scale computation with CAT12, you can either script the computation from Brainstorm and let it run sequentially overnight, or execute multiple CAT12 instances directly (not through Brainstorm) in parallel and then import sequentially the CAT12 output folders as full anatomy folders into the Brainstorm database.