I have a expert segmentation and i want to transform this file to GCA space. However, i first need to have the segmentation in conformed space cause the segmentation is 256x256x278 1mm and has a different origin. I tried the following:

>> mri_convert -rl orig.mgz -rt nearest mySeg.nii.gz mySeg_conformed.nii.gz

The output mySeg_conformed.nii.gz has now 256x256x256 voxels, although has a different origin than GCA atlas

Is there a command to set the origin to GCA's?

Thanks

2014-03-03 17:35 GMT+01:00 Bruce Fischl <fischl@nmr.mgh.harvard.edu>:

Hi Mohamed

the segmentations are in the individual subject "conformed" space. The talairach.m3z is what is used to transform GCA to the conformed coords

cheers
Bruce

On Mon, 3 Mar 2014, Mohamed Oualid Benkarim wrote:

Hi all,

I've performed FS subcortical segmentation and my purpose is to use these
segmentations as seeds to another method.
As FS uses GCA atlas to perform subcortical segmentation, I want to know if
the aseg.mgz output is in GCA atlas space,
or in original space except that the dimensions are 256x256x256, 1mm.

On the other hand, I also need to convert expert segmentations in native
space to GCA atlas space, that is, the inverse
of the process explained in
http://surfer.nmr.mgh.harvard.edu/fswiki/FsAnat-to-NativeAnat. I don't know
if there is a command to do so,
or we have to use a transformation matrix. In the latter case, FreeSurfer
creates several tranformation matrices: talairach.lta,
talairach.xfm, talairach.m3z....but it's is not clear which one I should
use.

Thank you in advance!!

The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.