Hello All,

I have got an issue with the procedure for dealing with a fail talairach registration. Failed talairach happen quite often for us. I go through the whole procedure of manually registering. 

I follow the procedure outlined in the URL. 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 on the procedure and how it even works..

In the step where we run 

tkregisterfv  --s tal_before --fstal 

When saving the transform it saves in the lta format. The file that need to be replaced is talairach.xfm. There is no way to save in a xfm format; if there is I could not figure it out. The talairach.lta is generated in the beginning of the autorecon2 step and is also a transform to register to a different target.  After running the recon-all transform.xfm does not update. I followed the direction. 

Furthermore, the part were your 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 registration. should the command be 

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

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