I tried editing the apar.2009a.aseg vpolume using 77 to fill in the lesions,
ran this code: recon-all -s ${subject} -autorecon2-cp this did not make any
difference.
________________________________
From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of
jennifer.fer...@alumni.ubc.ca [jennifer.fer...@alumni.ubc.ca]
Sent: Tuesday, March 31, 2015 11:30 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Accounting for lesions misclassified as non-brain
matter
________________________________
From: jennifer.fer...@alumni.ubc.ca
Sent: Tuesday, March 31, 2015 11:04 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Accounting for lesions misclassified as non-brain matter
Hi there,
I am having an issue with stroke lesions that border onto the cortex being
misclassfied by freesurfer. Often with lesions in this region the pial boudary
gets dragged to surround the lesion, missing actual grey matter and
inaccurately classifying the tissue.
The trouble is that every fix I can think of does nothing to impact this
misclassification.
I have tried:
filling in the lesion on wm.mgz (pictured here)
filling it in with voxels set to 110 on brainmask.mgz
and filling it in with voxels set to 77 (wm hypointensities) on apar.mgz
yet still this problem persists. Are there any other fixes I can use to correct
this issue?
Alternately if this issue can't be corrected should I expect it to impact my
data much? These lesions typically occur in the insula, but I am only
interested in quantifying primary motor and sensory areas, so will the
estimation of volumes in these areas still be accurate?
Thanks for any insight anyone can provide!
- Jenn
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