# Processing of volumes prior to dwipreproc

**URL:** https://community.mrtrix.org/t/processing-of-volumes-prior-to-dwipreproc/2112
**Category:** Uncategorized
**Tags:** preprocessing
**Created:** [December 7, 2018, 6:04am UTC](https://community.mrtrix.org/t/processing-of-volumes-prior-to-dwipreproc/2112 "2018-12-07T06:04:09Z")
**Posts on this page:** 1
**Showing post:** 7

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### 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: [June 28, 2020, 1:44am UTC](https://community.mrtrix.org/t/processing-of-volumes-prior-to-dwipreproc/2112/7 "2020-06-28T01:44:13Z")

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> > omit the denoising step from processing of just that set of volumes

> What set of volumes are you referring to here?

This is in reference to whatever set of images are to be provided to FSL `topup` via the `-se_epi` option. But the wording is maybe clumsy; that’s me trying to avoid writing an essay in every thread :-/

Let’s suppose the situation is (as it sounds applies to your case), that you have:

1. Phase encoding AP: 1 _b_=0, 60 _b_=3000 volumes;
2. Phase encoding PA: 1 _b_=0.

, and the tools you have at your disposal are:

- `dwidenoise`;
- `mrdegibbs`;
- `dwifslpreproc`;
- All other _MRtrix3_ utilities.

The question is: What data do you provide to each command, and in what order?

1. If you run all the phase encoding AP data through `dwidenoise` and `mrdegibbs`, then extract the solitary _b_=0 volume and concatenate it with the PA _b_=0 volume, then you have a situation where `topup` is estimating an inhomogeneity field where one volume has a different noise level than the other, and one has had Gibbs ringing removed whereas the other has not. This may cause issues, it may not.  
(You could also run the PA _b_=0 image through `mrdegibbs` here)

2. If you concatenate the PA _b_=0 image with the AP volumes, then run the whole lot through `dwidenoise | mrdebiggs`, you have the advantage that the same processing has been applied to both volumes that `topup` will be utilising; the disadvantage is that noise level estimation may not be quite right for the PA volume if spatial distortions are large, and AFAIK nobody has pursued quantifying just how deleterious this may be.

3. Extract the AP _b_=0 image _as the first step_, concatenate it with the PA _b_=0 image, and call it _X_; you then feed all AP data through `dwidenoise | mrdegibbs`, that forms the input image to `dwifslpreproc`; you could then feed _X_ through `mrdegibbs` if you wished, but you can’t run `dwidenoise` on it as there are too few volumes, that’s then provided via the `-se_epi` option to `dwifslpreproc`. The input volumes to `topup` have now had identical processing applied to them, so there’s no known bias to speak of; but the level of noise in those images is higher than it may otherwise be.

I would say there is not currently a consensus on which of these options is preferable. Personally I’m moving away from acquisitions like this so it’s less of a concern… But for retrospective data the question has been raised a few times and I don’t think any evidence was presented for one approach over the others.

Rob

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