Hi,

I'm trying to skip the reconstruction step in the diffusion toolkit and upload my own .nii file which already has an odf reconstruction and a vector of spherical harmonic coefficients for each voxel in the same format as the Loni MiND spherical harmonic scheme.  In order to use the tracking tool in the diffusion toolkit, it looks for _odf.nii , _dwi.nii, and _max.nii which should have been created in the first reconstruction step of the toolkit.  Do I need to create my own versions of these to satisfy the algorithm.  Also when I choose a mask of my own, like a general FA map, it looks for a certain header which is undefined.

Basically, the two tools of the diffusion toolkit GUI can be checked or unchecked.  What do I need in order to skip the reconstruction step and go straight to tracking with my own nifti dataset.

Thanks

E

Hi Ruopeng,

Does the tracking step require all of the mentioned .nii files output by the reconstruction?  Is the Diffusion Toolkit compatible with the spherical harmonic extension described by Loni MiND?  If so, then at each voxel there will be a vector of sh coefficients, which is not described in the _odf.nii file.   What is needed to create a .trk file using this scheme?

Thanks

E