Dear FSL Group, Prof.Smith
I will be much obliged if you could weigh in on the following question.
In practice there are subtle variations in acquiring DWI data. Examples include different combinations :
1. Short DWI scans (30 directions) about 6 mins.
2. Longer duration (say 128 directions) about 18 mins.
3. Multiple averages acquired sequentially with a break in between.
4. Repetitions (averages) part of the same pulse sequence.
Specific Condition:
My question pertains to post-processing one such combination: Two independent (but identical for averaging), long duration (15 min) scans with a break in between to check on the subject.
The subjects (patient population) likely readjusted in-between the scans as I talked to them between the two scans, even though we had cautioned them against moving their heads a priori. This in my opinion, is potentially a significant, source of motion in addition to the expected within scan motion.
Options from this list :
I have carefully studied both : Option (A) averaging the two acquisitons following 'eddy_correction' and Option (B) bvec rotation on eddy corrected concatenated data. These options appear to be suited for short duration, repetitions with limited patient motion between acquisitions.
Question :
My question is given my specific DWI acquisition variation, perhaps it is better to treat the two scans independently (as they really are), by eddy_correcting them separately. I could them compute DTI measures (FA, MD etc.) for each run and then combine them by co-registering and averaging them for each subject.
Thank you in advance for your time,
M Kumar
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