Thanks for the response. How do I go about uploading the subject?

On Monday, July 28, 2014, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote:

Hi Matt

certainly something is wrong, but it's hard to tell why from the single slice. You have big topological defects that are being fixed incorrectly. Can you upload the subject and we will take a look?
cheers
Bruce
On Mon, 28 Jul 2014, Walton, Matt wrote:

Hello Freesurfer team,
I've used freesurfer to segment (recon-all) approximately 30 different
subjects from a study. I've noticed that a large number of these subjects
have a misclassification of the white and pial boundaries in the occipital
lobe (such that grey matter is being classified as white matter). I believe
this problem is originating from my scanner and original data. I'm acquiring
a T1W BRAVO sequence on a GE Discovery 750w 3T scanner, using a 32 channel
phased array head coil. For many subjects, this acquistion gives intensity
inhomogeneity in the occipital lobe. I've begun using a GE based correction
technique (PURE) on the images, and it appears to improve the intensity in
the occipital lobe, but Freesurfer is still frequently misclassifying.

I'm wondering what would be the best way to edit the data. I've often tried
to edit the wm.vol, but this doesn't seem to fix anything. For the most
part, the wm.vol is correct to begin with, but the wm cutting line isn't
segmenting with the wm.vol. I've also tried to add control points but this
doesn't seem to improve anything either.

I've attached an image which I hope will further explain my problems.

Thanks for any help