# proc steps to dwi2fod output and next steps

**URL:** <https://community.mrtrix.org/t/proc-steps-to-dwi2fod-output-and-next-steps/3986>\
**Category:** Uncategorized\
**Tags:** dwi2fod, preprocessing\
**Created:** [August 5, 2020, 7:20am UTC](https://community.mrtrix.org/t/proc-steps-to-dwi2fod-output-and-next-steps/3986 "2020-08-05T07:20:55Z")\
**Posts on this page:** 2\
**Page:** 1

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**Author:** ![veeus18](https://community.mrtrix.org/letter_avatar_proxy/v4/letter/v/8c91f0/32.png) [@veeus18](https://community.mrtrix.org/u/veeus18)\
**Post date:** [August 5, 2020, 7:20am UTC](https://community.mrtrix.org/t/proc-steps-to-dwi2fod-output-and-next-steps/3986/1 "2020-08-05T07:20:55Z")

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Hello, I really appreciate the amount of help available on this forum, thank you!  
I just started using mrtrix3 and was hoping someone could give feedback on below processing steps and dwi2fod output

The rawdata (dwi\_raw.mif) has resolution 1x1x2, 66 volumes, with 10 b0s and 56-dirs with b=1000;  
below is what I have done so far-

1. dwidenoise dwi\_raw.mif dwi\_deno.mif -noise noise.mif

2. mrdegibbs dwi\_deno.mif dwi\_deno\_unr.mif -axes 0,1

3. dwifslpreproc dwi\_deno\_unr.mif dwi\_den\_unr\_preproc.mif —nocleanup rpe\_none -pe\_dir AP -eddy\_options " --slm=linear" -fslgrad bvec bval

4. dwibiascorrect ants dwi\_den\_unr\_preproc.mif dwi\_den\_unr\_preproc\_unbiased.mif -bias bias.mif

5a) mrconvert dwi\_den\_unr\_preproc\_unbiased.mif dwi\_den\_unr\_preproc\_unbiased.nii

b) bet2 dwi\_den\_unr\_preproc\_unbiased.nii dwi\_den\_unr\_preproc\_unbiased\_masked.nii -m -f 0.7

c) mrconvert dwi\_den\_unr\_preproc\_unbiased\_masked.nii mask.mif

1. dwi2response tournier dwi\_den\_unr\_preproc\_unbiased.mif wm\_response\_tournier.txt

2. dwi2fod csd dwi\_den\_unr\_preproc\_unbiased.mif wm\_response\_tournier.txt fod.mif -mask mask

The output looks like below-

![coronal](https://community.mrtrix.org/uploads/default/original/2X/7/75a7a50f63f2bd227058b5918e7c3867f6a63c14.png) ![sag](https://community.mrtrix.org/uploads/default/original/2X/c/ca613a764bf45c9028c3958aaaaa506c0a63fe9a.png) ![axial](https://community.mrtrix.org/uploads/default/original/2X/8/8a8e23659234eef89dbf2cc8bfca258bca288d99.png)

First question is if I should modify any steps from 1-7 to improve this output?

Secondly my goal is do prob tractography and compute connectogram using a white matter atlas; is there a webpage that details the steps? I found the [https://osf.io/pm9ba/](https://osf.io/pm9ba/) page and [https://andysbrainbook.readthedocs.io/en/latest/MRtrix/MRtrix\_Introduction.html](https://andysbrainbook.readthedocs.io/en/latest/MRtrix/MRtrix_Introduction.html), but the former is for connectome multi-shell data, and the latter explains with freesurfer outputs; I would like to try an atlas based method.

Thanks so much!

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<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:** [August 23, 2020, 12:02pm UTC](https://community.mrtrix.org/t/proc-steps-to-dwi2fod-output-and-next-steps/3986/2 "2020-08-23T12:02:36Z")

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Welcome @veeus18!

The main variation your listed steps have from the current recommendations are the response function estimation and FOD calculation algorithm. The `dhollander` algorithm is generally recommended for response function estimation. "`dwi2fod csd` invokes the original CSD algorithm, which involves a “soft” non-negativity constraint (negative values are penalised) rather than the “hard” non-negativity constraint (negative values are forbidden) of the MSMT CSD algorithm. Despite the naming, the “multi-shell” algorithm can still be used with what’s considered “single-shell” data: with two unique _b_-values the data can be decomposed into two tissues, typically WM and CSF.

As far as connectome construction using a volume-based atlas, take a look at my [BIDS App](https://github.com/BIDS-Apps/MRtrix3_connectome) and see if your target parcellation is already supported there. I’ve not yet been able to finalise and release a decent volume of [changes](https://github.com/BIDS-Apps/MRtrix3_connectome/pull/62), so it’s a little out of date, but new parcellations are not too difficult to add. Otherwise you can check out the relevant [wiki post](https://community.mrtrix.org/t/use-of-volumetric-templates-parcellation-atlases/2253) which explains the underlying logic & steps.

Cheers  
Rob