Hmmm,
Actually using aseg.mgz works just fine (just tried this now), displays correctly on fslview. What I was really trying to do was convert aparc+aseg.mgz which does not provide the expected orientation in fslview. Does this mean aparc+aseg.mgz and aseg.mgz are in different spaces somehow?
For the aparc_aseg_mni152.nii.gz output, 1) the coronal image in fslview (top left) has the S/I labels upside down compared to the coronal slice, (or the coronal slice upside down compared to the S/I labels) 2) the sagittal image (top right) has the same S/I issue 3) the axial image (bottom left) has the A/P labels the opposite of the image slice.
Thanks for any advice
-roddy
________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Roderick McColl [Roderick.McColl@utsouthwestern.edu] Sent: Monday, November 04, 2013 3:37 PM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] convert (resample) fsaverage/mri/aseg.mgz into $FSLDIR Nifti with MNI152_T1_1mm target
I am obviously using mri_vol2vol incorrectly but I'm stumped.
Goal is to get the $SUBJECTS/fsaverage/mri/aseg.mgz file into the FSL MNI152 space to do some fslmaths.
From looking around it seemed the command to accomplish this is (inside $SUBJECTS/fsaverage/mri)
mri_vol2vol --targ $FSLDIR/data/standard/MNI152_T1_1mm.nii.gz \ --mov aseg.mgz --reg transforms/reg.mni152.1mm.dat --o asegmni152.nii.gz
which does execute but if I load asegmni152.nii.gz into fslview all of the orthogonal views are upside down.
There is something missing regarding the co-ordinate system but I'm not sure what.
Can anyone point me in the right direction?
Thanks
-roddy
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