Re: [Freesurfer] SAG FSPGR BRAVO Sequence

yes, you can add control points to the white matter if that's what's going on Bruce On Wed, 30 Oct 2013, Ashley Hannah wrote:

Can this be manually corrected?

On Wed, Oct 30, 2013 at 2:19 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: looks like a pretty severe bias field may be the source of much of your problems (plus some motion artifact) On Wed, 30 Oct 2013, Ashley Hannah wrote:

        Here are the tkmedit with overlay images.

        Thank you for your help!

        Ashley



        On Wed, Oct 30, 2013 at 12:40 PM, Bruce Fischl
        <fischl@nmr.mgh.harvard.edu>
        wrote:
              It's hard to tell anything from those images.
        We need to see
              surfaces over volumes in freeview or tkmedit
        Cheers
        Bruce

        On Oct 30, 2013, at 12:01 PM, Ashley Hannah
        <ahannah1510@gmail.com>
        wrote:

              For some reason the images will not display.
        Hopefully this works....


        On Wed, Oct 30, 2013 at 11:31 AM, Bruce Fischl
        <fischl@nmr.mgh.harvard.edu> wrote:
              Hi Ashley

              if you upload a dataset we'll take a look. I
        am
              surprised to hear that you are having
        problems. Can
              you post an example image?

              Bruce
              On Wed, 30 Oct 2013, Ashley Hannah wrote:

                    Hello, 
                    Has anyone processed a SAG FSPGR BRAVO
                    sequence successfully through
                    FreeSurfer?

                    When I run these images the program
                    finishes without error however the
                    output  in tksurfer is grossly
                    incorrect. 

                    Is there a way to adjust the parameters
                    for reading white and gray matter by
                    freesurfer (because BRAVO has a
                    different contrast, not as defined) so
                    that
                    regions and boundaries are parceled
                    correctly?

                    Thanks, 
                    --
                    Ashley




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              <SAGBravo2_07.png>

              <SAGBravo1_07.png>




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