Dear all,
I certainly did not mean to re-open the debate about the use of denoising and/or Gibbs ringing before running eddy, I was rather trying to make the point that the segmentation fault is likely NOT due to running dwidenoise. eddy seems to be pretty sensitive to minimal discrepancies in voxel size etc. so maybe something like that might be happening during denoising.
I also forgot to include the following reference to a recent paper describing the merits of running denoising and Gibbs ringing correction prior to using eddy:
Ades-Aron, B., Veraart, J., Kochunov, P., McGuire, S., Sherman, P., Kellner, E., … Fieremans, E. (2018). Evaluation of the accuracy and precision of the diffusion parameter EStImation with Gibbs and NoisE removal pipeline. NeuroImage , 183 , 532–543. [https://www.sciencedirect.com/science/article/pii/S1053811918306827?via%3Dihub]
Best,
Matthias