I am interested in isolating the corticobulbar tract, which does not exist in the TBSS or TRACULA atlases. So far, it seems my best bet is to use Freesurfer's dt_recon to use my custom surface labels as seeds for tractography. Has anyone used any other software that they can recommend?
While TRACULA has some interesting and unique abilities, it is quite limited since it is confined to the tracts that have been pre-defined. This is largely related to the method in which tracts are automatically identified, which is also based on a "normal" brain; therefore, it is also not ideal for tracking in structurally abnormal brains.
You can certainly use freesurfer ROIs for seeds in many diffusion packages. It somewhat depends on what you are actually looking for in your research. Keep in mind that TBSS is very different from many other methods of tractography!
For probablistic tractography, the FSL diffusion package is quite easy to use and allows use of freesurfer ROIs as seeds. If you are more interested in deterministic tractography, I have found DSI Studio to be great (also offers other methods of ODF modeling other than tensor, such as generalized q-sampling, that can give better results than DTI). MRTrix and DTI Studio are other popular diffusion packages.
You will need to determine which package best fits your needs and invest some time in learning the software from the available manuals/tutorials.
I use MRtrix3 for customised seed-based tractography. Basically, create your ROI seed in MNI space (or any template), warp your bzero to that template, apply the resulting transformation matrix to your seed but as an inverse warp. Use the output as your ROI seed. To complete this process, use flirt, fnirt, and then applywarp.
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