Hi
I have proceed my data and produced a significance map across all my subjects and this looks fine on the fsaverage inflated brain. To compare to some other results, I really need to wrap this map into standard MNI152 space.
To do this, I have used the following commands but with a problem at the end:
1. mri_surf2vol -sig.mgh -identity fsaverage -template ./fsaverage/mri/T1.mgz -hemi lh -o SIG.fsspace.mgz
2. mri_vol2vol -mov SIG.fsspace.mgz -targ /$FSL_DIR$/data/standard/MNI152_T1_2mm.nii.gz -o SIG_MNI.nii -interp nearest -reg /$FS_DIR$/average/mni152.register.dat
So the first step works fine and looking at it using tkmedit shows the surfer as a nice volume in the right place on the T1.mgz or brainmask.mgz for the average brain. After step 2, looking at the final MNI space file, it appears that is has been rotated 180 degrees through the transverse plane (left and right are correct but top and bottom have been flipped and so have anterior and posterior) and the map has also translated. All of the dimensions are correct but the 2 images do not line up. I can easily rotate the image so that all the axis agree with the normal image but then the map is quite a few slices too high compared to the MNI152 brain and I cannot be certain how far it has been shifted.
Any help would be appreciated.
Thanks
Tom
Almost right. Try this command (reversed mov and targ and added --inv):
mri_vol2vol --inv –targ SIG.fsspace.mgz –mov /$FSL_DIR$/data/standard/MNI152_T1_2mm.nii.gz –o SIG_MNI.nii –interp nearest –reg /$FS_DIR$/average/mni152.register.dat
I know, it is a little confusing
doug
On 03/11/2014 04:39 AM, Thomas Allan wrote:
Hi
I have proceed my data and produced a significance map across all my subjects and this looks fine on the fsaverage inflated brain. To compare to some other results, I really need to wrap this map into standard MNI152 space.
To do this, I have used the following commands but with a problem at the end:
1.mri_surf2vol –sig.mgh –identity fsaverage –template ./fsaverage/mri/T1.mgz –hemi lh –o SIG.fsspace.mgz
2.mri_vol2vol –mov SIG.fsspace.mgz –targ /$FSL_DIR$/data/standard/MNI152_T1_2mm.nii.gz –o SIG_MNI.nii –interp nearest –reg /$FS_DIR$/average/mni152.register.dat
So the first step works fine and looking at it using tkmedit shows the surfer as a nice volume in the right place on the T1.mgz or brainmask.mgz for the average brain. After step 2, looking at the final MNI space file, it appears that is has been rotated 180 degrees through the transverse plane (left and right are correct but top and bottom have been flipped and so have anterior and posterior) and the map has also translated. All of the dimensions are correct but the 2 images do not line up. I can easily rotate the image so that all the axis agree with the normal image but then the map is quite a few slices too high compared to the MNI152 brain and I cannot be certain how far it has been shifted.
Any help would be appreciated.
Thanks
Tom
_______________________________________________ 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 greve@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@nmr.mgh.harvard.edu
-
Douglas N Greve -
Thomas Allan