Dear ExploreDTI community,
I'm having some ongoing trouble with deciphering the SM/EPI/EC correction pipeline, and could some advice.
First - in the mat file calculation step, I had to permute the gradient components to Y X Z, and flip them to -x y z (based on the acquisition parameters and the radiologists' instructions).
The phase encoding direction in my scan is anterior>posterior.
Therefore - should I still define the deformation axes as [1 0 0], or should I change them to [0 1 0]?
Second - I'm performing a longitudinal analysis in my study. Each participant has 4 scans, which I rigidly co-registered to their respective T1w images, and masked the transformed data with the brain mask I BETed earlier.
After the SM/EPI/EC correction, I exported the FA images for each scan, co-registered them to the first scan, and created subject-wise mean FA images.
I did this to get rid of whatever intra-subject variability there is, before delving into network atlas analysis.
So, the second SM/EPI/EC correction was also rigid, and involved a single dataset. I chose 'FA' as the image type for co-registration.
Many of the images came out misshapen- either elongated, or missing significant portions of the ventral forebrain or the brainstem.
Considering the ELASTIX transforms the atlas to the individual images, rather than the other way around - it this step actually necessary? If so, what other options can I tweak to get this right?
I'm aware of the 'hack' suggesting co-registering each of the longitudinal scan to one of the single subject-specific T1 images, but I'd rather avoid the consequent frowns from my current thesis committee and future peer-reviewers.
Thanks in advance,