Thanks for your help. It is most appreciated.

I thought I would mention that these subjects are  quite young (3-4 years old). I've read a few posts that free surfer is not ideal for analyzing young subjects, so I am wondering if this might be causing some errors. Maybe there is a way to register to a paediatric template, or something?

As well the raw T1w images always have an intensity bias in the occipital lobe. I'm not sure if this is from the coil itself (32 channel phased array), or just from the young subject age. Do you think ramping up the normalization procedures in freesurfer would result in an improvement?

Thought I would just let you know this, incase it helps you.

Matt


On Thu, Aug 7, 2014 at 10:12 AM, Tirrell, Lee <LTIRRELL@mgh.harvard.edu> wrote:
Hi Matt,

Overall, I've made the following changes that have led to some improvements:
- Remove excess dura from the brainmask that hasn't been stripped away
- Erasing voxels from wm in areas where white matter should be, even if the voxels don't show up as what on the wm mask. (If you view the wm volume with the heat color map, and lower the mid parameter to zero, areas that you have deleted show up in red) 
- Control points to push out the pial surface

Specifically for the case I sent you, I added control points near 115, 89, 82 (+/- a few slices in the sagittal view) to move the pial surface out further.  The wm intensity is decreasing as it moves out along that strand, so adding control points in these areas will increase the values to help Freesurfer recognize it as part of the white matter surface.

Also, near 141, 116, 45 (sagittal view) there is a problem with the wm surface. I tried deleting wm voxels as mentioned above, but I don't think I was aggressive enough on the first attempt so it didn't help much.  I will try this again to see if it leads to further improvements.

Best,
Lee


On 08/06/2014 11:54 AM, Walton, Matt wrote:
Hey Bruce,

Thanks so much. If it would help, I could upload another subject, perhaps one with worse segmentation in the occipital lobe. I could also upload a raw T1 image sequence (Nifiti)

Matt


On Wed, Aug 6, 2014 at 9:48 AM, Tirrell, Lee <LTIRRELL@mgh.harvard.edu> wrote:
Hi Matt,

I've taken a look at the subject that you uploaded.  I initially deleted portions of the skull from the brainmask that weren't removed from coronal slices 101-109 (see screenshot), which led to some improvement.  I also edited the wm volume by deleting areas that were obviously not white matter, even if it didn't effect the white matter surface.  However, this didn't lead to much improvement.  The segmentation isn't as bad in this subject as in the screenshot that you sent originally, so this strategy may help in worse cases. 

I am going to take another look at it now to try to improve the segmentation further.

Best,
Lee

     
On 07/30/2014 12:21 PM, Walton, Matt wrote:
Hey Bruce,

I uploaded a subject that you requested a few days ago (problems with segmentation in the occipital lobe). I just wanted to make sure the file transferred successfully, and if you have had a change to analyze.

Thanks,

Matt


On Mon, Jul 28, 2014 at 5:48 PM, Walton, Matt <mt.walton@alumni.uleth.ca> wrote:
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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The information in this e-mail is intended only for the person to whom it is
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contains patient information, please contact the Partners Compliance HelpLine at
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