[Freesurfer] Question about Talairach

HiLauren, This should be the correct command: freeview -v tal_before/mri/T1.mgz -v tal_before/mri/brainmask.mgz:reg=transforms/talairach.xfm (so remove the part "001/mri/" before "transforms"). Best, Koene ___ Freesurfer mailing list Freesurfer@nm

[Freesurfer] Question about Talairach

Hello, I was following the instructions on the wiki to check the registrations on some subjects. I ran the following command from my subjects dir, to view subject 001: freeview -v 001/mri/T1.mgz 001/mri/brainmask.mgz:reg=00

Re: [Freesurfer] question about talairach transform used in skullstrip

Guang, brainmask.auto.mgz (and all the volume files produced in the recon-all stream) remain in native space. you can add -nowsatlas after -skullstrip to recon-all to see the results without the atlas (results differ depending on the input). the tal transforms are used only to align the atlas, a

[Freesurfer] question about talairach transform used in skullstrip

Hi, there, In the skullstrip step, mri_em_register command is called and a talairach_with_skull.lta file is produced. This lta file will be used in the following mri_watershed command. My questions are: (1) Once we got the brainmask.auto.mgz, which command we can use to inverse the