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

2013-11-05 Thread Douglas N Greve
urfer-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 wi

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

2013-11-04 Thread Douglas N Greve
u > [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 > Nift

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

2013-11-04 Thread Roderick McColl
, 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

Re: [Freesurfer] convert (resample) fsaverage/mri/aseg.mgz into $FSLDIR Nifti with MNI152_T1_1mm target

2013-11-04 Thread Douglas N Greve
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 i

Re: [Freesurfer] convert (resample) fsaverage/mri/aseg.mgz into $FSLDIR Nifti with MNI152_T1_1mm target

2013-11-04 Thread Bruce Fischl
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

[Freesurfer] convert (resample) fsaverage/mri/aseg.mgz into $FSLDIR Nifti with MNI152_T1_1mm target

2013-11-04 Thread Roderick McColl
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/da