Hi there!
Since this is my first time using FreeSurfer, I found it quite challenging to get the handle on the different coordinate systems used. My goal is to generate vtk files where the vtk cortical surface and the vtk fiber tracts are in the same space (for one individual subject).
Basically, I used recon-all to generate the cortical surfaces and trac-all to generate dtifit_FA.mgz and dtifit_V1.mgz for tractography in the original diffusion space.
I used the transformation matrices generated in dmri/xmfs to transfer the cortical surface into the diffusion space, but not of them seem to work. What I find quite confusing is that when I visualize the surface lh.pial and the anatomical image brainmask.mgz using FreeView they nicely overlap; however, after I convert lh.pial to lh.pial.vtk and brainmask.mgz to brainmask.mha and visualize them using Paraview, they are in different spaces.
To do so, I used the command line mri_surf2surf so the surface will overlay with brainmask.mha image when using Paraview, but none of the transformation matrices seems to warp the surface onto the anatomical (structural FreeSurfer) space. I also tried to warp it to the diffusion space and the anatomical original space, but it never overlapped with the images nested in these respective spaces. It is always floating somewhere else!
I would like to know which transformation I need to: 1. apply to have the VTK surface overlap with the brainmask.mha image in the anatomical space and, 2. apply another transformation to transfer the VTK surface to the diffusion space where I perform tractography.
Also, does TRACULA perfom whole brain tractography?
I really appreciate your help!
Kindly, Islem