If the source is the FSL standard brain, then use $FREESURFER_HOME/average/mni152.register.dat as the registration. See if that works at stage 4.
Lena Palaniyappan wrote: > 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 > > > 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. 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