Dear FSL list (MJ?),
As you may have guessed, I'm not a regular FSL user, but Chris (my PhD
student) is using it and wants to rotate his b-vectors. Derek Jones
says it's a good idea for tractography (
http://onlinelibrary.wiley.com/doi/10.1002/mrm.21890/pdf ). I'm
therefore wondering what the matrices are that are spat out by the
eddy current correction.
I'm guessing that the mapping from [i,j,k,1]' indices in the reference
scan, to those of the individual scans, is by one of the following
(where Q0 is the Q/M-form matrix of the reference, Qn is the Q/M-form
matrix of the individual scan, and T is the matrix written out to the
text file by the eddy-current correction). I'm just not sure which it
is.
1) inv(Qn)*T*Q0
2) inv(Qn)*inv(T)*Q0
3) T
4) inv(T)
Voxels are isotropic, so it's not easy to tell whether the Q matrices
are involved or not.
The individual scans have been aligned with the reference. The plan
is to compute [U,S,V]=svd(T(1:3,1:3)) and then reconstruct an SO(3)
matrix from R=U*V'. Because I'm not sure which way the matrices go, I
don't know whether rotation is better done using R*b, or R'*b.
Any hints would be appreciated.
All the best,
-John
|