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
>>
>>
>>
>>
>>
>>
>>
>
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