Hello,
is a (physician-level) tutorial available ? I mean something that explains how to proceed step by step (starting from DICOM/NFTI datasets up to the CSD tractography)…
Thanks 
Cesare
Hi, Caesar,
I thought I will throw in my two cents of opinion regarding this request.
I am a clinician myself, and have started using MRtrix and performing tractography since 5 years ago.
You can find step-by-step instruction in mrtrix documentation
For mrtrix 3: http://mrtrix.readthedocs.io/en/latest/
For mrtrix 2 (older version): http://jdtournier.github.io/mrtrix-0.2/
I found the documentation provides clear explanation and is easy to follow - for learning basic DWI preprocessing and steps to perform tractography.
If you encounter any problem following the documentation, then you can post a question on this forum.
I found this forum very resourceful. You can often find relevant Q/A topics in this forum.
PPL running the forum are extremely helpful, and prompt, and more importantly, I felt they cater to ALL level of users.
Hope this helps,
Happy MRtrixing…
Joseph
Thank you Joseph for your kindly answer.
I’ve been successful in doing the first steps following the documentation but then I started being confused (I found 0.2 ver doc more clear for a step by step help). This is why I posted that request.
I’ve actually successfully installed all the packages needed on the OS X platform and I tried to find a 0.2-like easy workflow (White matter tractography: Importing DW data > Data pre-processing >ROI selection > Performing fibretracking) but I found myself lost into the M(a)Rtrix documentation
I’ll try do do some deeper search into the documentation! I’m sure I’m missing something 
Yes, I have to agree that the tutorial for MRtrix 0.2 was a lot easier to follow… I’ll see what I can do to help. Part of the problem though is that MRtrix3 allows you to do so much more, it’s difficult to know what a tutorial should cover… But maybe at least a little more detail on running some simple tractography would help.
This perfectly sums up the meaning of my question 
I’m trying to figure out how to do some tractography (for pre-surgical planning) starting from a single shell with 32 or 64 gradient directions acquired at 1.5T (b value is 1000 and 800 respectively).
If I’m not wrong this is the workflow I should follow as first steps:
- dwipreproc
- dwi2mask (optional?)
- dwi2response (and shview to check the resulting function)
…but then I get lost
Should I than move to Fibre Orientation Distribution estimation? Am I supposed to use MRtrix3 for Tractrography reconstructions or will I need to export some data and use an external software such as TrackVis for the last steps?
Any help would be much appreciated? 
Hi @Caesar,
I would suggest starting with the beginner tutorial, which covers the requisite steps and their required order.
.MRtrix3 includes the capability of performing tractography (the tckgen command), and obviously we would advise using this as opposed to other packages, but obviously what tools you use is up to you. For manual targeted tracking / track editing, the ROI tool within mrview can be used to draw the ROIs that you need for constraining the reconstruction to whatever pathways you are interested in.
I doubt that other diffusion MRI software packages would be capable of performing tractography using the complete FOD information that MRtrix3 estimates. Exactly what information is used within a tractography algorithm will depend on the software package (and in our case even the different tracking algorithms within the tckgen command have different requirements in terms of what information you provide to them). So I would suggest starting with MRtrix3 tracking, and only go to the effort of exporting image information to some other software package if there is a strong motivation for doing so (and we’d probably be interested to know what such motivation might be so that we can provide a better software package!).
Rob