Hi Ruthger

I'll leave 1 for Nick or Doug. As for 2, the easiest thing to do is the put your lesion mask directly into the aseg.mgz and rerun the segstats. You can find the appropriate label in FreeSurferColorLUT.txt and just replace the voxels values in aseg.mgz that correspond to your mask with the lesion value.

cheers
Bruce


On Wed, 29 Jun 2011, Righart, Ruthger  Dr. wrote:

Dear Freesurfer experts,

I posted one week ago a question about the SupraTentorial Volume that is indicated in the aseg.stats but unfortunately did not receive any suggestions as yet.

1. SupraTentorial Vol. is defined as Cortex + CorticalWhiteMatter + SubCortGray (http://surfer.nmr.mgh.harvard.edu/fswiki/MorphometryStats) but when I sum up these columns myself from the aseg.stats I do not arrive at the exact value of
SupraTentorial Vol that is indicated in the same aseg.stats. For some of my subjects this value is higher, for some it is lower. What could be the reason for these differences? Is CSF and ventricle volume already subtracted from the SupraTentorial Volume?

2. Is it possible to exclude lesions from the volume-based measures by
incorporating a self-defined lesion mask for each subject?

Any help or suggestions is very much appreciated!

Ruthger Righart (PhD)

Institute for Stroke and Dementia Research (ISD)
Klinikum der Universität München
Max-Lebsche-Platz 30
81377 Munich | Germany

ruthger.righart@med.uni-muenchen.de



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