Print

---

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
>