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Hi,
I ran the mri_cvs_register between two subjectIDs with very good alignment between them. I had assumed that applying the outputted m3z transform, i.e.,final _CVSmorph_toTEMPLATE.m3z, to the moving subjectID (subjb) would normalize it to the target subjectID (subja). That is, the outputted image would be the same as the output image from mri_cvs_register ,final_CVSmorphed_toTEMPLAT_norm.mgz; however, the resulting image was totally out of alignment to the target subjectID. This is the command I had utilized to apply the m3z transform to the moving subjectID:
mri_convert -at /home/vinny/Tools/freesurfer/subjects/subjb/cvs/final_CVSmorph_tosubja.m3z subjb.nii.gz subjb-to-subja_morph.nii.gz
Thanks for your help,
Vinny