Hi MRTrix Experts,
I have some questions about the best course of action in regard to tractography for the dataset that I am currently working on!
Background: I have some DWI data for neonates. As they are so young, their WM & GM boundaries are not well-defined. I am interested in performing whole-brain tractography and do have an acceptable cortical WM mask from a DRAWEM segmentation. However, my primary region of interest (the cerebellum) has no WM boundaries in this mask, and would not acceptably be included in the seed unless I manually added it. I had previously assumed this meant that I should not perform ACT, as I would need to include the whole cerebellum as either WM or GM, with no boundary.
My hope is to do whole-brain tractography and then use tckedit to subset tracts between the cerebellum and other regions of interest, using the -include options with my masks. I am primarily interested in tracts that are seeded in the cerebellum.
Am I correct about ACT not being ideal without a GM/WM boundary within the cerebellum, as the cerebellum is my region of interest?
If I am going to use the WM as my seed in whole-brain tractography, should I include the entire cerebellum in the WM mask? This seems incorrect but I do not want to exclude the cerebellum as a seed, and that is the alternative.
Would using the cerebellum as a seed in whole-brain tractography be an acceptable alternative, or would this be directly contradictory to the step I would like to perform after tractography (tckedit)?
My apologies if I am mistaken in my logic. I have tried to think carefully about this, but I am new to using MRTRrix. I was leaning towards including the cerebellum in my WM mask and performing whole-brain tractography but was unsure of the potential ramifications in the resulting tractography.
Thank you in advance for your help,