September 6, 2017 at 10:32 pm #861
Sorry for the delay.
BDP refines the DWI mask that you provide to remove CSF region. Your logs and the fact that you have *.rearranged.b0s.nii result saved indicate that this step is crashing for the mask that you provided.
If you can share the mask we can run it here and tell you what went wrong. Masking methods used in BDP are heuristic approaches that can fail for certain cases.
Also, the following information will be helpful :
Did you use the same mask before when it ran successfully for you ?
Can you try running BDP without the DWI mask (no –dwi-mask) – Does it still throw an error ?