Hi Roddy, aparc+aseg.mgz and aseg.mgz are in the exact same space and the same command line should generate the same result. Does it display properly in tkmedit? If so and if you're having problems visualizing with fslview, contact the FSL crew. doug
On 11/04/2013 05:52 PM, Roderick McColl wrote: > > 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 > > ________________________________ > > 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 > > > 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. > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
