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Dear Freesurfer Experts,
I am using .annot files to extract parcellated vertex-wise morphometric
features from surf files (e.g., area value from ?h.area file). For each
vertex, I want to determine the parcel it belongs to and its associated
morphometric features. During this process, I exclude vertices labeled as
‘unknown’ or ‘medial wall’.
In addition to the aparc parcellation, I am also using other parcellations
computed on fsaverage. Therefore, I need to resample these parcellations
onto native surfaces. To do this, I am using commands such as the one below:
mri_surf2surf --srcsubject fsaverage \
--sval-annot ${SUBJECTS_DIR}/fsaverage/label/lh.test\
--trgsubject sub-test \
--trgsurfval ${SUBJECTS_DIR}/sub-test/label/lh.test \
--hemi lh
As a sanity check, I used the above command to resample the aparc
parcellation onto native surfaces (which is already done by recon-all).
However, when I use the .annot files generated by the above command to
extract morphometric features from surf files, I get a different number of
vertices than when I use the .annot files generated by recon-all. Is this
behavior expected? Am I doing something wrong?
Thank you for your time and attention.
Best,
Leo
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