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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://secure-web.cisco.com/1tTquAOvaBa_r6ZBzCLADmD9ApAh3Dvzisbj8VkDe2zVY6u... 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.
On Tuesday, September 22nd, 2026 at 1:05 PM, El_Duderino_422 El_Duderino_422@proton.me wrote:
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://secure-web.cisco.com/1tTquAOvaBa_r6ZBzCLADmD9ApAh3Dvzisbj8VkDe2zVY6u... 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.