Hi,
I'm afraid the required code is not released at the moment.
We will hopefully have something ready for doing this over the
next 6 months.
All the best,
Mark
On 26 May 2010, at 02:25, Kyle Kern wrote:
> Hi FSL experts,
> Sorry to repost, I am wondering if it is possible yet with the
> current FSL version to use a warp registration with FIRST and still
> be able to use the .bvars files to perform a surface shape analysis?
>
> (see below)
>
> thanks,
>
> Kyle Kern
>
>
>
> Hi,
>
> I have been trying to use FIRST with FNIRT as described in another
> post to get better segmentations:
>
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1003&L=FSL&P=R24263&1=FSL&9=A&J=on&d=No+Match%3BMatch%3BMatches&z=4
>
> In the few subjects that did not segment well with FIRST, I have
> been able to get better meshes/volumes by finding the warpfield to
> MNI space using fnirt, running run_first on the image in MNI space
> (using the identity transorm for the -t option) and then putting the
> meshes back into native space (run_mesh_utils --doWarpMesh -i
> warp_field -m mesh.vtk -o out.vtk, [I was surprised to find that it
> needed the native-->MNI warpfield and not the inverse]), and also
> converting the mesh to a volume (first_utils --meshToVol -m mesh.vtk
> -i t1_image.nii.gz -l fill_value -o output_name).
>
> However, is there a way to get the .bvars for the meshes back in
> native space since I will need these to perform shape analysis? I
> see the --MeshToBvars option in run_mesh_utils but I cannot figure
> out the proper way to use it. Or, alternatively, is there a way to
> run_first with a warpfield instead of an affine matrix so that the
> bvars created will list the warp field instead of the identity
> matrix? What is the best way to use fnirt with FIRST and still be
> able to perform the shape analysis?
>
> thanks,
>
> Kyle Kern
>
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