Hi,

The model building and fitting process used in FIRST guarantees
that the number of vertices is the same (for a given structure) in order
to be able to get correspondence.  This is critical for the whole method. 
So you always get the same number of vertices, independent of whether
the coordinates are in MNI space or native space.  What is stored
in the vtk files are coordinates in native space.  The vertex analysis
is based on bvars (not vtk files) which can be easily applied in either 
space
(although require the flirt matrices to get into native space).

I hope that helps clarify things.

All the best,
    Mark



j janssen wrote:
> all the meshes that are generated after run_first for a given 
> structure have the same number of vertices. does that mean that they 
> are saved in native space but thereafter aligned?
>
> thanks,
> -joost
>
>
> On Mon, Mar 16, 2009 at 1:49 PM, Mark Jenkinson <[log in to unmask] 
> <mailto:[log in to unmask]>> wrote:
>
>     Sorry - my mistake before.
>     The meshes are actually saved in the native space, and are
>     what would be used by the ReconNative option.  The model
>     is transformed into the native space at the beginning of the
>     segmentation.
>
>     All the best,
>            Mark
>
>
>
>     On 16 Mar 2009, at 11:12, Mark Jenkinson wrote:
>
>         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
>
>
>
>
>
>
>
>
>