Hi Nikhil,
this indicates a problem with the talairach.xfm computation. The ICV is computed from the Talairach transform (which basically determines how much stretching is needed to get this image to the talairach space where the ICV is approx known). There is no mask.
See http://www.freesurfer.net/fswiki/eTIV for a description and how to check if the talairach.xfm is OK, most likely it is off in your case.
Note also that there was a problem with the order in which things are computed in FS 5.1: http://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes There is a workaround for this problem: cd subjid/mri talairach_avi --i nu.mgz --xfm transforms/talairach.xfm recon-all -s subjid -segstats
Best, Martin
On Mon, 2012-09-17 at 10:47 -0400, Nikhil Chandra wrote:
Hi everyone,
We have run FreeSurfer on roughly 60 subjects for a study, and are noticing some strange discrepancies for intracranial volume in aseg.stats for 8 of them. Here is a subset of what we see in one of the "bad" aseg.stats files:
# Measure CorticalWhiteMatter, CorticalWhiteMatterVol, Total cortical white matter volume, 559928.546875, mm^3 # Measure TotalGray, TotalGrayVol, Total gray matter volume, 769545.059854, mm^3 # Measure IntraCranialVol, ICV, Intracranial Volume, 1263234.600914, mm^3
Here, the total volume of WM plus GM is 1,329,473.606729 mm^3, which exceeds the intracranial volume by 66,239.005815. This does not make sense - how can the volume of brain matter exceed the volume of the space that encompasses it?
Does FreeSurfer generate a mask of the estimated intracranial volume? We would like to superimpose it over the T1 to see how accurate the estimation is for these cases. Also, does the mask (if it exists) include the cerebellum?
Thank you for your help, Nikhil Chandra _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer