Hello I am new to MRtrix3. Could you please guide me to the processing of DTI tractography?

[scg92]

Hello, I am new to MRtrix3. Could you please guide me to the processing of DTI
tractography?

[Avanti_Shrikumar]

I have used Andy’s Brain Book in the past: MRtrix Introduction: Overview of Diffusion Imaging — Andy's Brain Book 1.0 documentation

But it doesn’t discuss group analysis, namely the need to use a common response function. That is discussed in this thread: Group analysis

Regarding group comparisons, my impression is that it is an evolving area and I have seen recommendations to multiply each connectome with the “mu” value output by SIFT2 (which was not explicitly mentioned in the thread above, but is discussed in the threads below):

Compare structural connectivity across subjects

Hi, I would like to investigate whether the differences between structural connectivity matrices across subjects imply a different response to tDCS. From literature I can’t find a ‘good practice’ to properly compare the SC in output from tck2connectome, or whether there is the necessity to normalize SC. So far, I normalize the wm fod with mtnormalise, then I filter the whole brain tractogram with tcksift2 and in the end I obtain the SC with tck2connectome. Shall I do something else in order t…

Inter-subject normalisation using mu

Hello, In my analysis, I have calculated the SC using the “tcksift2” command and subsequently multiplied the streamline weights by a proportionality coefficient (mu). I read this paper titled “Quantitative Streamlines Tractography: Methods and Inter-Subject Normalization,” where different methods for calculating mu have been discussed. I am confused about which equation is utilized to calculate mu in the “tcksfit2” command. Is the adjusted mu used in this calculation? If not, please suggest h…

From reading this paper on the topic, I think the connectome comparisons are still valid even if you don’t multiply each connectome with its mu proportionality coefficient, but the interpretation is different; without scaling by mu, the connectomes would represent relative proportions of white matter fibers within the subject, and scaling by mu is necessary to get them to represent an absolute measure of bundle capacity.

[lconcha]

The B.A.T.M.A.N. tutorial is a great resource to learn mrtrix!

[Konstantina]

Hi! I did the BATMAN tutorial step-by-step (OSF) in parallel with the videos of Andrew Jahn (https://www.youtube.com/watch?v=A9j9gbSwU2k&list=PLIQIswOrUH68Zi9SVDAdcUExpq2i6A2eD&index=1&ab_channel=AndrewJahn). They are almost the same but for some steps (co-registration and sift) I followed Andrew’s recommendations.

[storrisi]

I agree that the BATMAN tutorial is great. Just FYI it’s basically been updated this year in the form of a paper with 19-pages of supplemental info: Structural connectome construction using constrained spherical deconvolution in multi-shell diffusion-weighted magnetic resonance imaging | Nature Protocols