Hey Jesper, I tried to re-order the volumes so that b0 is first when converting from PAR/REC to .nii, but the dcm2niix tool does not create correct bvals/bvecs files that correspond to the changed order of volumes, and I don't know how to generate bvals/bvecs files otherwise.
I have another question about the output I pasted from before. If eddy is correctly detecting the b0 and using it as the reference space, why do we see more movement for volumes that are collected closer in time to the b0? In fact, all of the values in the first column don't make sense to me. It seems strange that the movement of each volume relative to the b0 (collected last) increases over time, i.e., estimated movement increases as the time of volume acquisition relative to b0, the reference space, decreases. It seems that we should see the opposite trend.
Thank you!
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