Hi, I am trying to manually check the talairach registration from recon-all using tkregister2, but it appears to be looking for files in <subjectname>talairach/mri/orig. This directory structure does not exist in my dataset.
The tutorial recommended the following command line:
*tkregister*2 --mgz --s <subjectname> --fstal --surf orig
--fstal Check and edit the talairach registration that was created during the FreeSurfer reconstruction. Sets the movable volume to be $SUBJECTS_DIR/talairach/mri/orig and sets the registration file to be $SUBJECTS_DIR/subjectid/transforms/talairach.xfm. User must have write permission to this file. Do not specify --reg with this flag. It is ok to specify --regheader with this flag. The format of the anatomical can be changed with --mgh or --mghz
My data is in /space/lucy/2/users/margo/subjects/avm002 and I am using the std environment.
Can I run this command without the --fstal? What should I specify as the target and movable volumes in that case?
Thank you, Margo