Dear Jie,
This is not a usual thing to do, so if all you want to do is vertex analysis
(where all meshes are in a standard space) then you don't need to do
this individually - you just need to follow the instructions on the webpage
for vertex analysis.
If you really do need to do this for some other reason then be aware that
the coordinates stored are "scaled radiological" coordinates - not a standard
coordinate system (as in NIFTI) but an internal FSL coordinate convention
(that pre-dates NIFTI). It is different from NIFTI voxel coords, from NIFTI
mm coords and from MNI space mm coords. If you still wish to proceed
then you can do the transform with run_mesh_utils: e.g.
run_mesh_utils -f head_to_std_sub.mat -m head-L_Thal_first.vtk -o outputmesh.vtk --doMeshReg
All the best,
Mark
On 21 Nov 2011, at 23:59, Jie Shi wrote:
> Hi, all. I have a question about FIRST. I knew that this command firstly registers an image onto a common template with FLIRT, which gives an affine transformation matrix. Given that the resulting vtk is in the native space, I suppose that with the matrix left multiplying each vertex's coordinate will change the mesh back into standard space. I have tried this but found that the matrix has enlarged the volume of the mesh due to a scaling operation. So I wonder if this is a correct method of transferring a mesh into standard space? Thanks a lot.
>
> Jie
|