Re: [Freesurfer] FW: convert (resample) fsaverage/mri/aseg.mgz into $FSLDIR Nifti with MNI152_T1_1mm target - aparc+aseg.mgz problem
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] FW: convert (resample) fsaverage/mri/aseg.mgz into $FSLDIR Nifti with MNI152_T1_1mm target - aparc+aseg.mgz problem
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/filed
