Hi Melanie

doing it in tkmedit (or freeview) would be doing it manually. But if you do it this way it should allow you to correct the resulting surfaces and such

cheers Bruce On Wed, 12 Feb 2014, Melanie Morrison wrote:

Thanks,Melanie Morrison

Begin forwarded message:

  From: Bruce Fischl <fischl@nmr.mgh.harvard.edu>
  Date: 12 February, 2014 1:21:56 PM EST
  To: Melanie Morrison <melanie.morrison@hotmail.com>
  Subject: RE: [Freesurfer] How to avoid tumour from being
  segmented out

  Hi Melanie

  can you cc the list so that others can answer?

  thanks
  Bruce
  On Wed, 12 Feb 2014, Melanie Morrison wrote:

        Thanks. I can just do this manually? Can I over lay
        this on my anatomical

        map somehow so I can manually outline the correct
        boundaries.

        > Date: Wed, 12 Feb 2014 11:51:14 -0500

        > From: fischl@nmr.mgh.harvard.edu

        > To: melanie.morrison@hotmail.com

        > CC: freesurfer@nmr.mgh.harvard.edu;
        astevens@nmr.mgh.harvard.edu

        > Subject: Re: [Freesurfer] How to avoid tumour from
        being segmented out

        >

        > Hi Melanie

        >

        > you should be able to fill it in in the wm.mgz
        volume in either tkmedit

        > or freeview (using 255 if in freeview - tkmedit
        will do this by default)

        >

        > cheers

        > Bruce

        > On

        > Wed, 12 Feb 2014, Melanie Morrison wrote:

        >

        > > Hi there,

        > >

        > > I am creating surfaces from my volume T1-weight
        scans so that I can run

        them

        > > in AFNI's SUMA program.

        > > Problem is that my tumour has been segmented out
        because its intensity

        and

        > > the intensity of its surround area is much lower
        that what is being

        > > segmented.

        > >

        > > How can I avoid this? Or edit this? I need my
        functional MRI data to be

        > > displayed around the tumour region which is now
        unfortunately cut out.

        > > (HELPP!!!)

        > >

        > >

        > > Thanks,

        > > Melanie Morrison

        > >

        > >

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