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nipreps / dmriprep

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.
https://www.nipreps.org/dmriprep
Apache License 2.0
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Rotating oblique volumes and bvecs #117

Open josephmje opened 3 years ago

josephmje commented 3 years ago

I've been doing more tractography lately and was getting really bad tract segmentation on a particular group of scans acquired on a Siemens Prisma. After talking to Yogeth Rathi's group and @mattcieslak , both noted that it could be an alignment issue.

Matt has also noticed something similar in the HBN dataset and has implemented a correction in qsiprep. I implemented a fix on our lab's data using a pipeline from Penn BBL.

However, going forward, I'm unsure how dmriprep handles rotating the bvecs. Is there a place already in the code that I should be modifying? @arokem @dPys @oesteban

This might also fix the error in #113

dPys commented 3 years ago

@josephmje This is probably what you're looking for: https://github.com/nipreps/dmriprep/blob/master/dmriprep/utils/vectors.py#L479-L485