I have multi-shell diffusion imaging data with b = 0 (7 directions), b = 700 (20 directions), b = 1000 (32 directions) and b = 2000 (62 directions) of patients 1-2 weeks post-stroke. I have ran all necessary preprocessing (denoising, unringing, motion and distortion correction), followed by dwi2response dhollander for response function estimation and dwi2fod msmt_csd for the estimation of FODs using constrained spherical deconvolution. I would like to run a whole-brain tractography using 5tt and sift, excluding the lesion.
I could use your input on the following:
I am a bit puzzled though which algorithm (deterministic or probabilistic) I should use. In our lab and in our field (aphasia) deterministic approaches seem to be preferred, although I read on the forum and your papers that probabilistic approaches are preferred. I’m also aware of the fact that it depends on what you want to do with the data. Ideally, the approach would be appropriate for either connectome construction followed by the network-based statistic approach to find a subnetwork correlated with some behavioural variable, or to find all connections between a ROI and the rest of the brain. I have tried SD_stream and iFOD2 so far but I’m not sure how to choose between both…
Number of streamlines. I am following the BATMAN protocol and there they use 10 000 000 streamlines. I am however not sure how much is a sensible amount? If I use a deterministic algorithm, the file size gets very big (17-32 GB).
Seeding. I have tried using (50) random seeds per voxel or using the GM-WM interface. When I use random seeds per voxel and I filter the number of streamlines to 200k (with tckedit -number 200k, for visualization purposes) there are almost no tracts in the right hemisphere (both with probabilistic and deterministic algorithms). I thought this could be due to the fact that there are maybe lots of short fibers where the lesion is, but it also happens when the lesion is excluded. It does not happen with the gm-wm seed. Any ideas on this? And, what is a more sensible seed?
Other options: for now I left the default values for most of the options, I once included min and max length of the fibers (20-400 mm). Would you recommend to manipulate other options as well?
I know these are a lot of questions, so I thank you in advance for your input!