Hi Alejandra

you can do:

mri_convert -rt nearest -rl rawavg.mgz aseg.mgz aseg.rawavg.mgz

this will put it back in the scanner coordinates. Note that all of our results are in subject space (not e.g. MNI), but they are in slightly different ("conformed") voxel coords.

cheers Bruce

p.s. -rt nearest means resample type is nearest neighbor, and -rl rawavg.mgz means reslice "like" the rawavg.mgz volume

On Wed, 20 Aug 2014, Alejandra Machado wrote:

Hello,

I was wondering if FS has an output mask (labelled volume) for each tissue types (gm+wm+venctricular_csf) that I can then turn into each subject's native space. I understand I can use aseg.mgz or even aparc+aseg.mgz and then run mri_label2vol. But then how do I get correspondent labelling for each subject in it's own native space?

Thanks, Alejandra

thank you Bruce and Douglas for your reply!

Alejandra

2014-08-20 13:07 GMT+02:00 Alejandra Machado amachfern@gmail.com:

Hello,

I was wondering if FS has an output mask (labelled volume) for each tissue types (gm+wm+venctricular_csf) that I can then turn into each subject's native space. I understand I can use aseg.mgz or even aparc+aseg.mgz and then run mri_label2vol. But then how do I get correspondent labelling for each subject in it's own native space?

Thanks, Alejandra