Steps of tractography on hybrid FODs
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Want to try running tractography using our hybrid FODs or use them for your own research? Here's a quick overview of how to run hybrid tractography in a few simple commands. 

The hybrid FODs are made openly available in NIFTI format via our website. The FODs are described using spherical harmonics, similar to the FODs output from constrained spherical decoonvolution in MRtrix. We provide FOD files at multiple resolutions: 0.4, 0.6 and 1mm isotropic. These outputs can be input into standard tractography pipelines. Here we provide an example using MRrtrix tckgen:

1. Generate the whole brain tractogram with the hybrid FODs

.. code-block:: console


        tckgen -algo iFOD2 -seed_image dwi_wmMask.nii.gz -mask dwi_wmMask_dilated.nii.gz -step 0.2 -cutoff 0.05 -maxlength 120 -minlength 5 hybrid_FODs.nii.gz tractogram.tck



2. Antomical masks (seed, target and exclusions masks) can then be used to isolate a specific tract of interest. 

.. code-block:: console


        tckedit -include mask_seed.nii.gz  -include mask_target.nii.gz -exclude mask_exclude.nii.gz tractogram.tck fiber.tck