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" <gr...@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 >> >> >> This message and any attachment are intended solely for the addressee >> and may contain confidential information. If you have received this >> message in error, please send it back to me, and immediately delete >> it. Please do not use, copy or disclose the information contained in >> this message or in any attachment. Any views or opinions expressed by >> the author of this email do not necessarily reflect the views of the >> University of Nottingham. >> >> This message has been checked for viruses but the contents of an >> attachment may still contain software viruses which could damage your >> computer system: you are advised to perform your own checks. Email >> communications with the University of Nottingham may be monitored as >> permitted by UK legislation. >> >> ------------------------------------------------------------------------ >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________________ 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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