deletions | additions       diff --git a/Freesurfer_uses_an_atlas_scaling__.tex b/Freesurfer_uses_an_atlas_scaling__.tex  index 3fe8eac..2f19298 100644  --- a/Freesurfer_uses_an_atlas_scaling__.tex  +++ b/Freesurfer_uses_an_atlas_scaling__.tex 
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Freesurfer uses an atlas scaling factor (ASF) to calculate the eTIV, so even though the ROI encompasses all others, it is not calculated in the same way as other ROIs (i.e. by counting the voxels inside the skull). Rather, it estimates a linear transformation to an atlas space (Talairach) and calculates the determinant of the transformation matrix, which correlates to ICV \cite{buckner2004unified}. So actually the mechanism behind the biases in eTIV are different than those behind other regional volumes (i.e. regional varaition in CNR and gradient distortions affect the boundary). Because of this, we have removed the eTIV results since it doesn't make sense to include this particular metric. However, as stated in the previous response, we used eTIV to QC scans, particularly in sites 4,6 and 11 and removed the 1 scan from each site that was causing the bad scan-rescan reliability. I've included the test retest reliability of eTIV to verify the QC, but I have excluded it from the scaling factor calculations and validations.