OK, try this cmd mri_vol2vol --mov $FSLDIR/data/standard/MNI152_T1_1mm.nii.gz --targ aseg.mgz --reg transforms/reg.mni152.1mm.dat --o aseg_mni152.nii.gz --inv --interp nearest
On 11/05/2013 06:49 PM, Roderick McColl wrote: > Sure, no problem. > > Run from within the folder $SUBJECTS/fsaverage/mri :- > > mri_vol2vol --targ $FSLDIR/data/standard/MNI152_T1_1mm.nii.gz --mov aseg.mgz > --reg transforms/reg.mni152.1mm.dat --o aseg_mni152.nii.gz > > mri_vol2vol --targ $FSLDIR/data/standard/MNI152_T1_1mm.nii.gz --mov > aparc+aseg.mgz --reg transforms/reg.mni152.1mm.dat --o > aparc_aseg_mni152.nii.gz > > -roddy > ________________________________________ > From: Douglas N Greve [gr...@nmr.mgh.harvard.edu] > Sent: Tuesday, November 05, 2013 5:21 PM > To: Roderick McColl; Freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] convert (resample) fsaverage/mri/aseg.mgz into > $FSLDIR Nifti with MNI152_T1_1mm target - aparc+aseg.mgz problem > > Can you send your command lines for both aparc+aseg and aseg? > doug > > ps. Please remember to post to the list and not to me personally. Thanks! > > > > On 11/05/2013 12:45 PM, Roderick McColl wrote: >> Actually does not display properly at least not in freeview. >> Slices are also upside down. >> Also the output dims are 256x256x256 and I was expecting 182x218x182 which >> are the dims >> For $FSLDIR/data/standard/MNI152_T1_1mm.nii.gz. >> But I agree that I should get in contact which the FSL people also. >> Thanks >> -roddy >> >> -----Original Message----- >> From: freesurfer-boun...@nmr.mgh.harvard.edu >> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve >> Sent: Monday, November 04, 2013 5:22 PM >> To: freesurfer@nmr.mgh.harvard.edu >> Subject: Re: [Freesurfer] convert (resample) fsaverage/mri/aseg.mgz into >> $FSLDIR Nifti with MNI152_T1_1mm target - aparc+aseg.mgz problem >> >> >> 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 >> >> >> > -- > 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 > > -- 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
