Hey Bruce. Thanks for the response. How do I go about uploading the subject?
On Monday, July 28, 2014, Bruce Fischl <fis...@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 >> >>
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