I suppose you could look for voxels that outside of the cortex and adjacent to it
On Wed, 11 Jul 2018, John Anderson wrote:

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Dear Dr Bruce,

Thank you for the response. Indeed, I was completely wrong, these represent a 
pathology and should
not correct for!

Kindly, I have one additional question not relevant to the subject of this 
email. Is there any way
in Freesurfer to create mask for the regions between the sulcuses. I want to 
compute PET signal in
these regions and normalize for it.

Thank you so much!

Hi John


why do you want to correct for them? They likely represent a pathological 
process, so correcting for
them may remove whatever effects you are looking for, no? The space between the 
sulci and the
ventricle volume won't directly affect surface-based analysis, but of course 
the sulcal widening
likely reflects cortical atrophy that will be



‐‐‐‐‐‐‐ Original Message ‐‐‐‐‐‐‐
On July 11, 2018 11:37 AM, John Anderson <john.ande...@protonmail.com> wrote:

      Dear Freesurfer experts,
I have two groups of subjects (healthy and patients). The patients have 
different degrees of
atrophy. Looking into the individual scans, the subjects are largely different 
in the space
between the sulcuses and the size of ventricles. My questions are:
1. Is there any way to correct for these differences in the surface based 
2. Including eTIV covariate does it help in this case?
3. Does the resampling to "fsaverage" overcome the challenge of these 
differences between the

I appreciate any advice,

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