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, and for user display in tkmedit and tksurfer.

Nick

On Tue, 2009-08-11 at 08:56 -0500, Guang Zeng wrote:

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 talairach transform, convert the coordinate to the original system?

(2) How different it will be if no altas is used in the mri_watershed step?

Thanks a lot!

Guang

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