Talairach (-<no>talairach)
This computes the affine transform from the orig volume to the MNI305 atlas using Avi Snyders 4dfp suite of image registration tools, through a FreeSurfer script called talairach_avi. Several of the downstream programs use talairach coordinates as seed points. You can/should check how good the talairach registration is using
tkregister2 --s subjid --fstal
You must have an "fsaverage" subject in your SUBJECTS_DIR. tkregister2 allows you to compare the orig volume against the talairach volume resampled into the orig space. If you modify the registration, it will change the talairach.xfm file. Your edits will be *not* be overwritten unless you run recon-all specifying -clean-tal. Run
tkregister2 --help
for more information. Creates the files mri/transform/talairach.auto.xfm and talairach.xfm. The flag -tal-check will check the registration against known-good transforms. Adding the flag -use-mritotal after -talairach will use the MINC program mritotal (see Collins, et al., 1994) to perform the transform.