I see. To clarify. orig is the conformed version of the original input file, which means just sampling to 1 mm as needed, and cropping to 256 matrix. norm.mgz has some intensity corrections, but does not include spatial changes.

I had read http://surfer.nmr.mgh.harvard.edu/fswiki/FsAnat-to-NativeAnat
and I thought that maybe that spatial warping was involved beyond resampling to the original dimensions/resolution to get to  "native space". This simplifies things greatly. Thank you both.


On Mon, Mar 25, 2013 at 1:56 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote:
Hi Josh,

there are no spatial transforms to go from orig to norm. They are in the same space.

cheers
Bruce


On Mon, 25 Mar 2013, Joshua Lee wrote:

Hi Doug,

Is a standard 12 affine registration sufficient to get a subjects structural
(in a different orientation) into the same space as norm.mgz, or will I need
some non-linear registration? Basically, what kind of transforms are applied
to go from orig to norm?
-
Joshua Lee
Graduate Student
Center for Mind and Brain &
Department of Psychology
University of California, Davis
530.747.3805


On Mon, Mar 25, 2013 at 10:52 AM, Joshua Lee <jkilee@ucdavis.edu> wrote:
      Hi Doug.
      That was in fact what I decided to do.

      Thanks!

      Josh
      -
J


On Mon, Mar 25, 2013 at 7:38 AM, Douglas N Greve
<greve@nmr.mgh.harvard.edu> wrote:

      Can you compute the registration between the manually
      traced anat space
      and the FS conformed space? Eg, with BBR. If you can do
      that, then you
      can run mri_label2vol to convert the mask into FS
      conformed space
      (assuming that that is what you want to do).
      doug

      On 03/22/2013 04:43 PM, Joshua Lee wrote:
      > Hi All,
      >
      > I wanted to get peoples advice on the best method of
      > registration/interpolation to use on a manually traced
      segmentation
      > (and its structural) that is not in the same space and
      orientation as
      > the structurals I started Freesurfer with (although they
      both
      > originally came from the same image. I want to maintain
      the integrity
      > of the manual traced binary mask through this
      registration and
      > reslice. For a number of reasons, I do not want to take
      Freesurfers
      > output to the space of the manual segmentation.
      >
      > What do people think is a good technique? Flirt nearest
      neighbor
      > interpolation? Something different from Freesurfer?
      ANTs?
      > -
      > Josh
      >
      >
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MGH-NMR Center
greve@nmr.mgh.harvard.edu
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