Hi everyone,
I am very new to all of this and I am hoping to get some eyes on what I’ve got so far to make sure it looks correct. I am working with scans from 3-month old infants, b=700 in 30 directions, b=0 in 5 directions and I’m following Andy’s tutorial.
I think the response functions from dwi2response dhollander look good, but I’m concerned about the FODs.
The FODs generated in the next step look a bit strange to me and don’t look like the example in Andy’s tutorial. As you can see, it looks like there is very little gray matter (top middle image; all of the participants look like this, with very little green). I used SS3T from MRtrix3Tissue and then overlaid the WM FODs on top of the combined image (top right image). Again, this image also does not look like the one from the tutorial.
The bottom row has the individual FODs for each tissue type (WM, GM, CSF):
I apologize for uploading them all as one image—it seems like as a ‘new user’ I can only include one attachment in my post, so I wasn’t able to attach each photo individually at this time.
For those that are more experienced and knowledgeable, do all of these images look okay? Why is there very little GM visible in the combined FOD image? Is this expected given the low b-value and that it’s infant brains? Is there some correction I should be doing, or do I just keep going with these scans as is? Any thoughts or advice is appreciated!
Thanks!
Taryn