________________________________ 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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