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-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Roderick McColl
[roderick.mcc...@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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