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!!
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