# Running a full MRTRIX processing pipeline from AP and PA DICOMS

**URL:** <https://community.mrtrix.org/t/running-a-full-mrtrix-processing-pipeline-from-ap-and-pa-dicoms/4327>\
**Category:** Uncategorized\
**Created:** [November 27, 2020, 12:33pm UTC](https://community.mrtrix.org/t/running-a-full-mrtrix-processing-pipeline-from-ap-and-pa-dicoms/4327 "2020-11-27T12:33:29Z")\
**Posts on this page:** 1\
**Showing post:** 8

<div class="post-metadata">

**Author:** ![rsmith](https://community.mrtrix.org/user_avatar/community.mrtrix.org/rsmith/32/2672_2.png) [@rsmith](https://community.mrtrix.org/u/rsmith)\
**Post date:** [February 21, 2022, 11:45pm UTC](https://community.mrtrix.org/t/running-a-full-mrtrix-processing-pipeline-from-ap-and-pa-dicoms/4327/8 "2022-02-21T23:45:00Z")

</div>

Hi Mags,

Daan gave [a good response to this question in another thread](https://community.mrtrix.org/t/preferred-dwi-denoising-pipeline/5556/2). The original question there does not cover the prospect of having an adequate number of DWIs in multiple phase encoding directions independently, but the point regarding EPI distortions making the spatial distribution of noise not quite equivalent between phase encoding directions holds here. Personally I’ve historically just concatenated everything together then denoised, but I trust Daan’s judgement here moreso than my own. It’s also a common source of uncertainty, so might be worth turning into a Wiki page.

Cheers  
Rob

---

_[View the full topic](https://community.mrtrix.org/t/running-a-full-mrtrix-processing-pipeline-from-ap-and-pa-dicoms/4327)._