Hi Joan,
The aseg.mgz file is the actual segmentation volume. FreeSurferColorLUT.txt is simply a text look up table with label numbers, colors, and identifying tags. In the most recent versions of Freesurfer you do not need to include this in your command line, it will open with this automatically, but if you wanted to specify the look up table you would do so after the segmentation volume: -segmentation <volume> <lookup table>
As for the aseg.stats, not sure why it's empty. This is a simple text file (more or cat will open it) - but there is nothing there? Have you tried to just run: recon-all -segstats -s <subjid>
Jenni
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Joan Fisher Sent: Sunday, March 25, 2007 10:09 PM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] aseg.stats
It turns out that the segmentation is fine in aseg.mgz (although for some reason I am unable to view the segmentation with FreeSurferColorLUT.txt as it says it wasn't valid or wasn't found even though it is in my directory) and yet the aseg.stats table was not generated.
(Doug?) How does one generate a table if the aseg.mgz file is accurate but the aseg.stats file is not?
Many thanks, Joan
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