Hi list, I need to create a mask of frontal, parietal, temporal and occipital lobes in a subject by using cortical parcellation output. Is it possible? Eventually, how can I transform these masks file to mii.gz (to import them in FSL analysis). Thank you very much. Regards,
Stefano
you can use mri_binarize on aparc+aseg, eg, something like
mri_binarize --i aparc+aseg.mgz --match 1003 1012 1014 1032 --o frontal.nii.gz
those numbers come from $FREESURFER_HOME/FreeSurferColorLUT.txt That table has a lot of ROIs in it, and not all will be in the aparc+aseg. You'll be interested in the ones between 1000-1035 and 2000-2035
doug
On 09/04/2013 08:46 AM, stdp82@virgilio.it wrote:
Hi list,
I need to create a mask of frontal, parietal, temporal and occipital lobes in a subject by using cortical parcellation output.
Is it possible? Eventually, how can I transform these masks file to mii.gz (to import them in FSL analysis).
Thank you very much.
Regards,
Stefano
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Stefano, Take a look at the lobe mapping section on this wiki page. Example commands near the end.
https://surfer.nmr.mgh.harvard.edu/fswiki/CorticalParcellation
-Louis
On Wed, 4 Sep 2013, stdp82@virgilio.it wrote:
Hi list, I need to create a mask of frontal, parietal, temporal and occipital lobes in a subject by using cortical parcellation output.
Is it possible? Eventually, how can I transform these masks file to mii.gz (to import them in FSL analysis).
Thank you very much.
Regards,
Stefano
freesurfer@nmr.mgh.harvard.edu
-
Douglas N Greve -
Louis Nicholas Vinke -
stdp82＠virgilio.it