Doug, thanks So, is this a correct sequence:
Im extracting thickness measures from VBM contrasts generated by FSL VBM analysis (this is 2X2X2):
1. To convert VBM contrast file to a binary mask:
mri_binarize --i vbmcontrast.nii.gz --o vbmmask.nii --min 0.95 --max 1 (for fsl vbm generated corrp maps, where values are stored as 1-p, min 0.95 identifies all voxels with p less than 0.05)
2. to check if this mask lies in appropriate place on fsaverage image:
tkmedit -f fsaverage/mri/T1.mgz -overlay vbmmask.nii -fthresh 0.5
3. to register groupaverage with fsaverage fslregister --s fsaverage --mov groupaverage/mri/T1.mgz --reg threshreg.dat
4. to view it on the fsaverage volume
tkmedit fsaverage T1.mgz -overlay vbmmask.nii -overlay-reg threshreg.dat fthresh 0.5 -surface lh.white -aux-surface rh.white
5. to map it on the fsaverage SURFACE
mri_vol2surf --mov $SUBJECTS_DIR/vbmmask.nii --reg $SUBJECTS_DIR/threshreg.dat --projdist-max 0 1 0.1 --interp nearest --hemi lh --out lh.fsaverage.masked.mgh --reshape
6. to view it on the surface
tksurfer fsaverage lh inflated -overlay lh.fsaverage.masked.mgh -fthresh 1
But I am seeing the surface projections on completely different regions than when using FSL templates to view the VBM contrast
Cheers Lena
On 20/08/2010 20:41, "Douglas N Greve" greve@nmr.mgh.harvard.edu wrote:
You'll have to sample that mask onto the surface using mri_vol2surf with the --interp nearest option. You will also have to have a registration matrix, which will depend on where the volume came from.
doug
Lena Palaniyappan wrote:
I have a mask file which I need to overlay on the individual images of a group of subjects to extract thickness values within ht mask. But the mask is of dimension 2X2X2, will this be an issue?
Thanks Lena _______________________________________________________ *Lena Palaniyappan *Clinical Lecturer & Honorary StR | Division of Psychiatry ( University of Nottingham) South Block 'A' floor| Queens Medical Centre | Nottingham | NG7 2UH
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_______________________________________________________ Lena Palaniyappan Clinical Lecturer & Honorary StR | Division of Psychiatry ( University of Nottingham) South Block 'A' floor| Queens Medical Centre | Nottingham | NG7 2UH