eek, that's pretty awful. If you upload the subject dir we will take a look
cheers
Bruce
On Thu, 30 Jun 2016, Katherine Reiter wrote:

Dear FreeSurfer experts,
I am working on a data set and am having particular difficulty with one
subject. It appeared the skull strip was mistakenly removing occipital
regions. These regions were absent from the brainmask, T1, and resulting
surfaces. I attempted to solve this in 2 different ways. I first adjusted
the watershed and reran the recon-all -autorecon2 in order to redraw the
surfaces. Adjusting the watershed worked to include these regions in both
the brainmask and T1 but the resulting surfaces hugely inaccurate (see the
attached screenshot  '4003_badsurfs_parietal_cerebellum2'; Oddly enough, the
frontal surfaces are largely accurate but the parietal regions include gray
matter in the white surface and even large amounts of the cerebellum, while
excluding occipital regions.

I then reran it from the raw dicoms and had the same issue with occipital
regions being excluded so I adjusted the watershed and tried to manually fix
the surfaces, but this resulted in similar inaccurate surfaces. See the
second attached screenshot '4003_badsurfs'. ll surfaces are fairly messy,
but some regions are more accurage, where the appears to distinguish between
gray and white and other areas are over inclusive, but cerebellar and some
superior and medial regions are excluded. 

Any and all help would be much appreciated. Thanks in advance!
Kate

Katherine Reiter, M.S.

Clinical Psychology Doctoral Student

Marquette University

Phone: (414) 288-3807Email: katherine.reiter@marquette.edu

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