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Hello All,

I have dMRI data collected on a Siemens Prisma machine as follows:

Two shells (b=700 and 2000) with opposite PE directions (AP and PA
respectively) and a different number of diffusion gradients (89 and 90
respectively) but the number of b0 volumes are the same for both shells (7
b0 volumes collected at the beginning of each shell).

I wonder which of the following ways you recommend to correct for EC,
Susceptibility, and motion correction:

1-
a) using "topup" to estimate the susceptibility map.
b) use "eddy" with the first shell only as the input (--imain=b700).
c) use "eddy" with the second shell only as the input (--imain=b2000).
d) use "fslmerge" to merge the eddy corrected outputs of steps b and c.
e) using "paste" to merge the bval and rotated bvec files from steps b and
c into one bval and bvec file.

or

2)
a) using "topup" to estimate the susceptibility map.
b) use "fslmerge" to merge the two shells as b700_2000.
c) using "paste" to merge the bval and bvec files of the two shells into
one bval and bvec file.
d) use "eddy" with the merged shells as the input (--imain=b700_2000) and
bval and bvec files of the above step.


Thank you!
Mahmoud