Hi, I’m trying to run an FBA with some historical GRE dti images.
I have run basic preprocessing (motion, distortion, susceptibilty, and bias field (eddy) correction) with a local pipeline.
From there, I have run and QCed dwidenoise, mrdegibbs, dwi2response dhollander. I have used the -fslgrad option throughout.
Response functions and voxel assignment looked similar to BATMAN tutorial.
At this stage, as I have a patient group and control group, I wasn’t sure whether to create group specific response means or overall average. I have done both.
I then upsampled with mrgrid
I had some trouble with have holes in my masks, but got around this by using FSL bet for mask creation (as advised on some other threads here).
I have QCed at each of these steps and everything looked fine to me.
However, when running dwi2fod, my FODs came out looking very strange and not at all like the tutorial or anything else I’ve seen.
Any help with troubleshooting would be really appreciated!