bbregister --s <subj> --mov <volid> --reg <regfile> \
- This program performs within-subject, cross-modal registration using a boundary-based cost function. The registration is constrained to be 6 DOF (rigid). It is required that you have an anatomical scan of the subject that has been analyzed in freesurfer.
REQUIRED FLAGGED ARGUMENTS
- --s subject
FreeSurfer subject name as found in $SUBJECTS_DIR.
- "Moveable" volume. This is the template for the cross-modal volume. Eg, for fMRI, it is the volume used for motion correction.
Output FreeSurfer registration file (tkregister-style or LTA format).
- Include B0 distortion correction while performing registration. A voxel shift map can be created from a B0 map
with the epidewarp.fsl script (in FreeSurfer)
Initialize the FreeSurfer mri_coreg program.
- Do NOT use aparc+aseg.mgz as a reference mask. It will not attempt to use aparc+aseg if it is not there.