I am sorry; my previous email had a few grammatical errors that made it hard for even me to understand.

Hello all,

I have an issue with the procedure for dealing with a failed Talairach registration. Failed Talairach registrations happen quite often for us. I go through the whole procedure of manually registering as outlined in https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach_freeview. This never seems to work. Yesterday, I did some digging, and I am a bit confused about the procedure and how it even works. First, I should say that I am using FreeSurfer 7.3.2 on an Ubuntu 20.04 system.

In the step where we run

tkregisterfv --s tal_before --fstal

when saving the transform, I always assumed I should overwrite the talairach.lta file, since it can only save an .lta file, and assumed that recon-all would convert it to talairach.xfm. There is no way to save in .xfm format using tkregisterfv; if there is, I could not figure it out.

I realized that I am doing something wrong when I noticed that talairach.lta is generated at the beginning of the autorecon2 step and is also a transform to register to a different target. After running recon-all, transform.xfm does not update.

Separately, in the part where you check the registration with the command:

freeview -v tal_before/mri/T1.mgz -v tal_before/mri/brainmask.mgz:reg=tal_before/mri/transforms/talairach.xfm

T1.mgz and brainmask.mgz are always in register. Once you do a transformation on the brainmask, it will always be out of register. So should the command instead be:

freeview -v fsaverage/mri/T1.mgz -v tal_before/mri/T1.mgz:reg=tal_before/mri/transforms/talairach.xfm

Please correct me — I know I am completely misunderstanding things.