Hello!
I am relatively new to tractography so was looking for some help with my pipeline. I am looking to do cerebellar specific tractography and collect microstructural data (FA, MD, AD and RD). I saw that tckgen is the first command followed by ‘sift2’, ‘tckstat’ ‘tcksample’, is this correct? Could you please advise me on how to go about this.
Secondly, I wanted to analyse the white matter tracts in the cerebellum. I was given a script for a different brain region but wanted to know how I can do the white matter tract analysis for the cerebellum.
The proper sequence of commands will depend on the details of your experiment to a greater level of detail than what’s currently provided here. For instance, if the last step in your pipeline were to be tcksample, which can produce sampled values of microstructural data along streamlines trajectories, it is unclear how the weights determined by the SIFT2 algorithm would be integrated into that analysis.
“Analyze white matter tracts” is also unfortunately ambiguous. For instance, I could interpret this as a connectome-style analysis, where the cerebellum is parcellated into many regions and you wish to evaluate those microstructural measures along the streamlines trajectories connecting those regions, or this could be an along-tract analysis, which involves capturing the values of those measures as a function of distance from one streamline endpoint to the other, rather than collapsing that spatial contrast. Maybe if you could link to a manuscript that echoes the kind of analysis you wish to perform?
There’s certainly nothing in MRtrix3 that’s hard-wired for brain data and will produce an error if it “doesn’t look like a brain”.