Tutorial for Physicians!


#1

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 :slight_smile:

Cesare


Mrtrix3 installation on windows 7 platform
#2

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


#3

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 :slight_smile:

I’ll try do do some deeper search into the documentation! I’m sure I’m missing something :thumbsup:


#4

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.


#5

This perfectly sums up the meaning of my question :smile:


#6

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 :slight_smile:

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? :thinking: