Re: [Freesurfer] transforming aseg.mgz, brain.mgz to native scanner space and dimensions

Hi Mario

from the mri dir:

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

should do the trick

cheers Bruce On Thu, 16 Feb 2012, Mario Ortega wrote:

Hello Freesurfer Mailing list,

I would like to know how to do the item mentioned in the subject> Ideally not just write out the brain and aseg regions into isotropic voxels in standard space, but also accomplish converting back to the original resolution, would I have to specify an inverse transform file? If I follow the directions in the mri_label2vol, I get volumes in a scanner like orientation, but not the correct x,y,z, dimensions. Ie, I get 256x 256 x 256 as x,y,z. When in fact we scan at 256x256x176

Thanks Mario