That flag is to perform only the subcortical segmentation, but there are are steps leading up to it that need to be done. If all you want is a subcortical seg, then you can just run
mri_synthseg --i orig.mgz --o synthseg.mgz

On 1/15/2025 8:42 AM, Sara Rapuc wrote:

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Dear all,

I ran FS recon-all -subcortseg -sd -subjid and it was completed without any errors. However, when looking into the mri folder, there is no aseg.mgz file, only aseg.auto.mgz. Could you please explain why this is and how to get the aseg.mgz file?

Thank you.

Best wishes,

Sara
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