dMRIPrep is a robust and easy-to-use pipeline for preprocessing of diverse dMRI data. The transparent workflow dispenses of manual intervention, thereby ensuring the reproducibility of the results.
So, the heavy lifting is done. It seems pretty stable and does a good job.
Some points though:
It doesn't include freesurfer's reconall. There seems to be an issue with running reconall even without combining it with the diffusion preprocessing pipeline. It doesn't trouble me since we generally use freesurfer outside nipreps since they don't include new versions of it.
I still need to work on applying transformation matrices to the DWI image. Shouldn't be an issue.
After all building blocks will be set, I will create a new version of DerivativesDataSink to standardize the naming scheme of the pipeline's outputs.
So, the heavy lifting is done. It seems pretty stable and does a good job. Some points though: