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
________________________________
UT Southwestern Medical Center The future of medicine, today.
Hi Roddy
can you check whether fslview shows the directions as correct even if it displays it upside down? That is, do they still know which direction is superior, anterior, etc...?
cheers Bruce
On Mon, 4 Nov 2013, Roderick McColl wrote:
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
UT Southwestern Medical Center The future of medicine, today.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
try this command instead
mri_vol2vol --mov $FSLDIR/data/standard/MNI152_T1_1mm.nii.gz \ --targ aseg.mgz --inv --reg transforms/reg.mni152.1mm.dat --o asegmni152.nii.gz
On 11/04/2013 04:37 PM, Roderick McColl wrote:
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
UT Southwestern Medical Center The future of medicine, today.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
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Bruce Fischl -
Douglas N Greve -
Roderick McColl