If I prefer not to use qudec, can I instead use mris_preproc to do the registration to atlas and concatenate the files and then use mri_surf2sruf to smooth? And then proceed with inferential statistics?

Thank  you!

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from the wiki:

The primary output file is ?h.pial_lgi, which can be viewed as an overlay in tksurfer or freeview:

tksurfer my_subject_id lh inflated -overlay lh.pial_lgi

To perform a vertex-wise analysis in QDEC of the lgi surface data, first sample the results to the average template subject 'fsaverage':

recon-all -s my_subject_id -qcache -measure pial_lgi

Do this for each of the subjects in your group




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