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Rotating oblique volumes and bvecs #117

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josephmje opened this issue Sep 15, 2020 · 1 comment
Open

Rotating oblique volumes and bvecs #117

josephmje opened this issue Sep 15, 2020 · 1 comment
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@josephmje
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josephmje commented Sep 15, 2020

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

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dPys commented Sep 15, 2020

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

@oesteban oesteban added this to the 0.4.0 milestone Oct 13, 2020
@oesteban oesteban modified the milestones: 0.4.0, 0.5.0 Dec 10, 2020
@josephmje josephmje self-assigned this Dec 18, 2020
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