Hi, I have a couple questions about this procedure which I came across in the discussion
forum.
I have 2 repetitions of the same DTI sequence to increase the signal gained. I have
concatenated my bvals and bvecs and ran eddy_correct on the merged file ( lining the
brain s up with the -t option in fslmerge).
It is recommend in the post here to " then rotate the bvecs by the rotation part of the flirt
transformation matrices that are stored in the ecclog. I think you should be able to
do this by simply multiplying each bvec by the top 3x3 matrix in the
flirt matrix for that volume"
May I ask if you mean multiply each bvec number by the TOP LEFT 3x3 matrix as there
are 4x4 matrix in the ecclog for each volume?
Secondly would this step be mandatory and would it be less accurate in my
DTIFIT/BEDPOST procedure if I did not rotate the bvecs as mentioned above? It is noted
on the email post that it is presumed the two brains are at different angles at each
repetition of the sequence. How much motion would be required (from one repetition to
another repetition) to do this above step of rotating the bvecs? Visually when I check the
B0 images from each repetition, some subjects have a noticeable shift in between the
repetitions while others has same positioning of the brain in both repetitions.
I used the MCFLIRT function on the FEAT option to check the level of motion in the merged
file. The rotation is upto 0.04 rad and the translation 2-5mm. It mentioned high level of
motion detected with the merged file. Is the rotation more important than the translation
movement detected, to decide if I need to perform this step of multiplying each bvec by
the 3x3 matrix in the ecclog for DTIFIT/BEDPOST procedure?
If the pre-stats report did not have high level of motion detected, would it be safe to
concatenate the same bvecs (without rotating) to do the the DTIFIT/BEDPOST procedures
required for tractography analysis?
Many Thanks in advance
Siewmin
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