Hi Matt
there are instructions on our wiki. You can either ftp or use the
filedrop, although ftp is probably best if you are uploading an entire
subject
cheers
Bruce
On Mon, 28 Jul 2014, Walton, Matt wrote:
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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