use mri_aparc2aseg instead of label2vol. This is how aparc+aseg.mgz is created. Look in the recon-all.log file for the command line used.

doug

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-fr...

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

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