MRtrix tutorial available on OSF


Hi to all MRtrix3 users!

I just wanted to share some resources with you: At this year’s MICCAI conference, there was a contest on the best tutorial. For that, I wrote a step-by-step tutorial on MRtrix3, which explains how you analyze raw multi-shell DWI data. In there, you’ll learn how to:

  1. preprocess the data, and get some idea of what the purpose of each of the analysis steps is,
  2. create a whole-brain tractogram and filter out specific tracts of interest,
  3. create a structural connectivity matrix,
  4. use the connectome visualization tool.

Additionally, I’m providing tutorial data – both the raw dicom data as well as any files which are to be created throughout the tutorial. Throughout the tutorial, I’m providing example code which can be directly used on that test data.

If you want to find out more, just visit the OSF tutorial website:

Thanks and enjoy,



It’s really cool. very helpful, thanks!


Thank you for your feedback, @zonglei, glad you can make use of it :+1:


Hi @martahedl
MRtrix3 doc tell us to run mrgibbs first, and then run dwidenoise because the former may change the noise structure( But I noticed you reverse their order in your tutorial. Do you think which order is better?


@Zonglei The wording of the description in mrdegibbs can be misleading. “This command” in the following refers to mrdegibbs: “Similarly, if you intend running dwidenoise, you should run this command afterwards, since it has the potential to alter the noise structure, which would impact on dwidenoise’s performance.” So denoising should be performed before mrdegibbs.


Thanks @maxpietsch for clarifying this :slight_smile:
@zonglei: Thanks for paying attention. If anything else seems unclear, don’t hesitate to bring it up!


First of all, awesome tutorial. I really appreciate the amount of effort that your team is investing into this tutorial.

I am a medical student without any background in computing, trying to learn MRtrix with this tutorial.

I am current facing an issue with page 6 of the BATMAN_tutorial, step 2.2

I tried following with the details as follow:

Arthurs-MacBook-Pro:DWI arthur$ dwidenoise dwi_raw.mif dwi_den.mif –noise noise.mif

dwidenoise: [ERROR] Expected exactly 2 arguments (4 supplied)

dwidenoise: [ERROR] Usage: dwidenoise dwi out

dwidenoise: [ERROR] Yours: dwidenoise dwi_raw.mif dwi_den.mif –noise noise.mif

May I know if I have missed out on anything?

Thank you



If you copy and pasted the code into a terminal there is a chance that the ‘-’ before ‘noise’ is a dash instead of a minus sign. Try typing this character into the terminal instead.


Awesome. Thanks for the help! :slight_smile: