Hello! I have a rather general question to the DWI experts here on which steps to consider when applying mrtrix to high-resolution ex-vivo (single or multi-shell) animal data.
I read Problem with dwi2response msmt_5tt (amp2response) command for ex-vivo monkey data, Estimate response function for multi-shell ex-vivo marmoset data and Multi-tissue CSD and it seems that the mrtrix steps of response function estimation and FOD fitting can be used in a rather straight-forward way on non-human data as well. In general terms, is that also the case for tractography and track density estimation (eg. SIFT2)?
I would like to quantitatively compare the connectomes of different animals and humans (data very similar or identical in quality to the links above) - right now I’m generating 5tt segmentations semi-manually for each animal (I merge sub-cortical and cortical gray matter as per this comment), use 3-tissue (dhollander (2019)/msmt_csd on multishell or MRtrix3Tissue dhollander/ss3t_csd_beta1 for single shell data) CSD for FOD estimating, run tractography using dynamic seeding and compute sift2 weights for the resulting tracts (20M). I then compute a sift2-weighted TDIs for quality control and extract tracts using masks of subcortical structures (thalamic nulcei etc.) as selection masks in tckedit.
Now, as I’m by no means an expert in MR/diffusion phyics, I was wondering if and to what degree this processing is valid in ex-vivo data of different species, and what would need to be done to make the processing more quantitative. I know this is a very broad topic…