Re: [Freesurfer] rendering problem

Hi Gabriel - We don't develop slicer, so we don't know what the assumptions are but here's where you can find their tutorials, if that helps: http://www.slicer.org/slicerWiki/index.php/Slicer_3.6:Training

If you scroll down you'll find the one on importing freesurfer files.

a.y

On Wed, 18 Jan 2012, Gabriel Gonzalez Escamilla wrote:

Yes, I did, they answer me just before you, and told me that exist a tutorial but, that was made time ago, so they're not sure if any of the assumptions that went into making the tutorial have changed. Do you know anything about it??

Regards, Gabriel.

El 18/01/12, Bruce Fischl fischl@nmr.mgh.harvard.edu escribió: Hi Gabriel,

  have you asked the slicer folks about this?

  Bruce
  On Wed, 18 Jan 2012, Gabriel
  Gonzalez Escamilla wrote:

  > Dear FS experts,
  >
  > I'm trying to render the surfaces and volumetric data from FS
  into
  > 3D-slicer, Because I've read on the net that is compatible with
  FS surfs and
  > images; but something seem to be not right, I'm sending you an
  attached jpg
  > with my problem.
  >
  > The thing is that I've load the ?h.pial surface (gary render)
  and the
  > rawavg.mgz (gray-scale) and compare them with the original
  NIfTi images
  > (green render) which I've obtain from the reconstruction of the
  dicom files;
  > and is the image I'd used in FS to create the 001.mgz image as
  input for the
  > recon-all processes.
  >
  > As you may see in the attached image, each time I do load the
  images they
  > appear to be in different spaces, but they're supposed to be in
  the subjects
  > native space,
  > apparentely the mismatching between the two images (in 3D
  slicer) starts
  > from the conversion from NIfTI to the 001.mgz image; Because
  when I load it
  > into slicer is in the same space as the rawavg.mgz and the
  other mgz images
  > Is it a problem when images loading in slicer or could I've
  been doing
  > something wrong?
  >
  > And I don't really have idea for the mismatching between the
  surfaces and
  > the mgz images.
  >
  > I have created a fiber vtk file in another program, and the
  fibers load in
  > the same space as the NIfTI volume, which makes me think that
  the NIfTI has
  > been loaded correctly.
  >
  > Bests,
  > Gabriel.
  >
  >
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--

PhD. student Gabriel González-Escamilla Laboratory of Functional Neuroscience Department of Physiology, Anatomy, and Cell Biology University Pablo de Olavide Ctra. de Utrera, Km.1 41013 - Seville

• Spain -

Email: ggonesc@upo.es http://www.upo.es/neuroaging/es/