Hi all,
I am interested in projecting my functional connectivity z map to the cortical surface. I attempted to use mri_vol2surf but received a warning message (see command and output below) indicating that the voxel resolution in the source volume doesn't match the registration file. Perhaps as a result of this, when I attempt to load the resulting .mgh file in tksurfer, nothing appears on the cortical surface image. Any idea what went wrong?
Thanks in advance, Kevin
Here's the my command and output:
mri_vol2surf --mov N89_L_WholeAmyMask_g7_zfrm_avg.nii.gz --reg $FREESURFER_HOME/average/mni152.register.dat --hemi lh --trgsubject fsaverage --out lh.L_WholeAmy_buckner_YC.mgh --projfrac 1 --surf-fwhm 4 srcvol = N89_L_WholeAmyMask_g7_zfrm_avg.nii.gz srcreg = /usr/local/freesurfer/stable5_0_0/average/mni152.register.dat srcregold = 0 srcwarp unspecified surf = white hemi = lh trgsubject = fsaverage surfreg = sphere.reg ProjFrac = 1 thickness = thickness reshape = 0 interp = nearest float2int = round GetProjMax = 0 INFO: float2int code = 0 Done loading volume WARNING: the voxel resolution in the source volume (2,2,2) differs from that listed in the registration file (1,1,1) Reading surface /space/sake/3/users/inverse/subjects/fsaverage/surf/lh.white Done reading source surface Reading thickness /space/sake/3/users/inverse/subjects/fsaverage/surf/lh.thickness Done Mapping Source Volume onto Source Subject Surface 1 1 1 1 using old Done mapping volume to surface Number of source voxels hit = 23569 Surface smoothing by fwhm = 4 (n=12) Writing to lh.L_WholeAmy_buckner_YC.mgh Dim: 163842 1 1
Hi Kevin, you can ignore that warning. The values in the registration file are not correct.
doug
ps. you can verify that the registration is correct with:
tkregister2 --mov $FSLDIR/data/standard/MNI152_T1_2mm.nii.gz \ --reg $FREESURFER_HOME/average/mni152.register.dat --surfs
On 4/26/11 1:11 PM, kevin bickart wrote:
Hi all,
I am interested in projecting my functional connectivity z map to the cortical surface. I attempted to use mri_vol2surf but received a warning message (see command and output below) indicating that the voxel resolution in the source volume doesn't match the registration file. Perhaps as a result of this, when I attempt to load the resulting .mgh file in tksurfer, nothing appears on the cortical surface image. Any idea what went wrong?
Thanks in advance, Kevin
Here's the my command and output:
mri_vol2surf --mov N89_L_WholeAmyMask_g7_zfrm_avg.nii.gz --reg $FREESURFER_HOME/average/mni152.register.dat --hemi lh --trgsubject fsaverage --out lh.L_WholeAmy_buckner_YC.mgh --projfrac 1 --surf-fwhm 4 srcvol = N89_L_WholeAmyMask_g7_zfrm_avg.nii.gz srcreg = /usr/local/freesurfer/stable5_0_0/average/mni152.register.dat srcregold = 0 srcwarp unspecified surf = white hemi = lh trgsubject = fsaverage surfreg = sphere.reg ProjFrac = 1 thickness = thickness reshape = 0 interp = nearest float2int = round GetProjMax = 0 INFO: float2int code = 0 Done loading volume WARNING: the voxel resolution in the source volume (2,2,2) differs from that listed in the registration file (1,1,1) Reading surface /space/sake/3/users/inverse/subjects/fsaverage/surf/lh.white Done reading source surface Reading thickness /space/sake/3/users/inverse/subjects/fsaverage/surf/lh.thickness Done Mapping Source Volume onto Source Subject Surface 1 1 1 1 using old Done mapping volume to surface Number of source voxels hit = 23569 Surface smoothing by fwhm = 4 (n=12) Writing to lh.L_WholeAmy_buckner_YC.mgh Dim: 163842 1 1
-- Kevin Bickart MD-PhD Student Department of Anatomy and Neurobiology Boston University School of Medicine
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kevin bickart