I have a set of dMRI images with me. For me to get started with the fiber tractography how do I get the ground truths?
Next question is how to generate the tensors from DWI image. I read from papers that DTI method for generating tensors suffers when the fibers are crossing.
Is is that for the ground truth do we have to derive ourselves on our own synthetically? How do we do that and what are the file extensions for the ground truths?
I’m new to DTI myself so hopefully someone else will come in and confirm what I’m about to say
Firstly, not sure what exactly you mean by “ground truths”. Are you referring to b0 volumes? (volumes taken with diffusion weighting, b, set to 0) If so, I don’t think having just these volumes by themselves will do you any good; they’re mostly used for comparisons
How you get the b0 volumes, calculate tensors, etc. is through any one of many, many software packages. FSL, freesurfer, dipy, qsiprep, DSI Studio are all common DTI packages. DSI Studio is probably the most beginner friendly.
If your data is still raw off the scanner, you should put it into .nii format using dcm2niix
Crossing fibers cause problems, yes. There are some common DWI approaches that specifically try to account for that difficulty, e.g. q-ball imaging. Read more here: https://pubmed.ncbi.nlm.nih.gov/23486659/
Actually why I referred to ground truth is that suppose that an algorithms spits out a particular pathway how do we validate that the path spit out by the algorithm. So for validating the pathway we need some ground truth right?