btw, you should not need to run mri_annotation2label twice. On 11/21/2013 10:44 AM, Mojdeh Zamyadi wrote: > Hi all, > > I want to convert the cortical labels I get in freeSurfer to volumetric > ROIs in the subject space and I've followed the steps mentioned in: > http://brainybehavior.com/neuroimaging/2010/05/converting-cortical-labels-from-freesurfer-to-volumetric-masks/ > > except since I'm interested in lobe mapping I've changed the first > commands, more specifically these are the different command I've run: > > 1. mri_annotation2label --subject P2 --hemi lh --outdir > freeSurfer_Results/P2/labels/ --lobesStrict > freeSurfer_Results/P2/labels/freeSurfer_lobes > > 2. mri_annotation2label --hemi lh --subject P2 --outdir > freeSurfer_Results/P2/labels/ --annotation > freeSurfer_Results/P2/labels/lh.freeSurfer_lobes.annot > > 3. tkregister2 --mov freeSurfer_Results/P2/mri/rawavg.mgz --noedit --s > P2 --regheader --reg freeSurfer_Results/P2/register.dat > > 4. mri_label2vol --label freeSurfer_Results/P2/labels/lh.parietal.label > --temp freeSurfer_Results/P2/mri/rawavg.mgz --subject P2 --hemi lh --o > freeSurfer_Results/P2/labels/lh.parietal.nii.gz --proj frac 0 1 .1 > --fillthresh 1 --reg freeSurfer_Results/P2/register.dat > > the issue I have now is that the final ROI I get (e.g. > "lh.parietal.nii.gz") looks like a series of disconnected points! I was > wondering how I can get a smooth (i.e. filled) volumetric ROI? > > Thanks, > -Mojdeh > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >
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