you'll need to get the code associated with each lobe. You can do this by running tkmedit subject nu.mgz -seg lobeseg.mgz -aux lobeseg.mgz
This will show colors for the seg, but the names will be wrong. Click on a seg and see what number it gets in the aux. Then create a new color table to match, then run mri_segstats
doug
On 05/07/2014 04:51 PM, pfotiad@nmr.mgh.harvard.edu wrote:
Hi Doug,
Thanks for your help, the mri_aparc2aseg command worked fine. In addition, is there a way to get a binary volume for each of the lobes based on the result of the mri_aparc2aseg command? In other parcellation volumes, I would use mri_binarize and the FreeSurferColorLUT.txt table but here I coudn't think how this could be applicable.
Thanks again, Panos
Try using mri_aparc2aseg instead of label2vol. See the --help and/or look in the recon-all.log file to get the command line used to create the aparc+aseg.mgz file doug
On 05/07/2014 11:12 AM, pfotiad@nmr.mgh.harvard.edu wrote:
Hi FS Community,
I created a lobes annotation file with the --lobesStrict flag of the mri_annotation2label and then converted it to a volume with the mri_label2vol command and the --annot flag. However, the resulting volume is just overlapping on top of the white surface, and not on the whole cortex. Is there a way to create a volume for the lobes that covers the whole cerebral cortex? That is a volume that shows you which part of the cerebral cortex belongs to each of the 6 lobes individually?
Thank you in advance, Panos _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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