Hi,
Going to and from "volumes" where these are just a collection of the
vertices in a 1D order and applying FDR on this is fine, since FDR
does not use any spatial information when calculating its correction.
This is why it is the easiest to implement in this case, since the
volume
representation does lose all spatial information, but for FDR this does
not matter.
The mesh coordinates are all saved in MNI space (the space of the
model) for the vtk files. When you perform vertex analysis in native
space it transforms these coordinates before doing the vertex analysis.
Writing transformed meshes can be done using the --doMeshReg
option with the -f option to specify the flirt matrix (the option usage
message for this is currently not correct). However, this won't give
quite
the same space as that used for the useReconNative and useRigidAlign
options, as these alignments are calculated internally to the vertex
analysis.
It is probably worth waiting for a few days, if you can, since we are
going
to release a patch with several changes in FIRST. In particular, we
have
substantially improved the statistical sensitivity of the vertex
analysis. We also
will have easier options for performing many of the steps for vertex
analysis
and FDR correction.
All the best,
Mark
On 16 Mar 2009, at 09:18, j janssen wrote:
> Dear all,
>
> 1st point: some time ago i got code to do FDR correction after
> vertex-wise analysis with FIRST. actually, the FDR was applied to
> images, not surfaces, as FDR was not implemented yet in
> run_mesh_utils.
>
> - is the FDR correction, i.e. going from surfaces to volumes,
> applying FDR to volumes, and going back to surfaces valid?
>
> 2nd point: run_first for a given structure and multiple subjects
> generates .vtk's for the given structure. i noticed that the meshes
> are not in native space but aligned.
>
> - in which space are the meshes saved by run_first?
>
> - i used first_utils with -vertexAnalysis --useReconNative --
> useRigidAlign, works fine. however, i would like to write out the
> individual meshes, in native space and rigid aligned (--
> useReconNative --useRigidAlign). how would i go about this?
>
> thanks,
> -joost
>
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