Hey Bruce.

 I've sent one of my subjects in which I noticed the segmentation problems in the occipital lobe. Sagittal slice 115 provides a good example. I've also noticed that with my subjects I frequently have problems with segmentation of the temporal lobes, although adding control points usually fixes this quite well.

Thanks for your help

Matt

On Mon, Jul 28, 2014 at 3:22 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote:

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 <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

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