Re: [Freesurfer] (no subject)

I guess you'll need to run a set of individual steps in recon-all, and probably need to edit the file to disable e.g. talairach and aseg On Wed, 8 May 2013, Shani Ben Amitay wrote:

Ok-will tryAny  idea how can I avoid steps like aligning to atlas when running specific steps of the streamline?

On Wed, May 8, 2013 at 4:24 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: oh, that's going to be tough. I guess you could extract the WM and use it to create our wm.mgz and go from there On Wed, 8 May 2013, Shani Ben Amitay wrote:

  Segmentation into white matter gray matter and CSF of a rat brainCan you give me brief
  directions-where to
  start from?

  Thanks!

  Shani


  On Wed, May 8, 2013 at 3:46 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote:
        Hi Shani

        what kind of segmentation? In general yes, but you'll need to mess with the recon-all
  script

        cheers
        Bruce
        On Wed, 8 May 2013, Shani Ben Amitay wrote:

              Hello Freesurfer
              I would like to extract the stream for surface-based analysis on the output of an
              in-house segmentation
              process.Is this possible?How?

              Thanks

              Shani




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