Hi James

I did, and one of our RAs here is going to be looking into it. Louis (ccd) can give you more information

cheers
Bruce

On Tue, 15 Jul 2014, james pardon wrote:

Hi Bruce,
I was wondering whether you have seen my email below?

Thanks so much

Cheers,
James


On Sat, Jul 12, 2014 at 9:18 AM, james pardon <james.pardon15@gmail.com>
wrote:
      Hi Bruce,
I have sent the link for a problem subject via a private
message. Please note since MS causes hypointense lesions in white
matter I have used an algorithm that fills hypointense lesions in WM
with median intensity of normal appearing WM.

Thanks
James


On Fri, Jul 11, 2014 at 11:19 PM, Bruce Fischl
<fischl@nmr.mgh.harvard.edu> wrote:
      Hi James

      if you upload a problem subject we will take a look (the
      whole subject dir please)
      cheers
      Bruce
      On Fri, 11 Jul 2014, james pardon wrote:

            Hi all, 
            On a few subjects with a specific pathology
            (MS) I cannot easily reconstruct temporal
            lobes.
            I think this issue comes up quite regularly on
            the mailing list, and I have tried to trouble
            shoot using control points, WM edits, even
            getting back to orig/001.mgz to correct areas
            that
            may seem the culprit for breaking surface
            reconstruction. Some subjects have gone
            through 7-8
            runs of recon-all with different edits but
            still the problem persists in a few subjects
            in my
            study. 

            I have also tried to use -mprage and -3T flags
            along the way to allow more liberal control
            point growing, despite an improvement in my
            results some of subjects still have very bad
            surface constructions. I have attached two
            snapshots to this email and I am happy to
            upload
            the complete subject folder if you need to
            take a look at them. 

            As far as the SNR is concerned, I have
            designed my study based on recommended
            Freesurfer
            parameters a couple of years ago on 3T Siemens
            Trio with 32-channel receiver coil. 

            A huge thank you for your previous helps, and
            thanks in advance for helping me with this new
            issue.

            James


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