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:
External Email - Use Caution
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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