Hello MRtrix experts,
I’m a MRtrix , FBA beginner and I need your help regarding the illustration of FBA results.
I have followed the FBA steps which work very well and I am really happy with my results.
Can someone please explain to me how can I obtain the whole brain template-derived tractogram that is shown systematically in FBA papers ?
I attached the image that I’m obtaining of the FOD templates it doesn’t look like the basic template derived tractogram and I’m really upset about it…
Is it a threshold, additional command lines or supplementary parameters to compute the whole brain template derived tractogram? Or there is any file that correspond to derived tractogram ?
Thank you in advance for you help !
Looking forward to hearing from you !
Not sure what the problem is if you successfully completed a fba analysis,(Fibre density and cross-section - Multi-tissue CSD — MRtrix3 3.0 documentation),
since you should also have generated a whole brain tractogram .tck file (steps 19 and 20 in the documentation). The .tck file can be overlayed via the tools/tractography menu
Please remember to load the reduced set of tracts (step 20)
Something else to consider/ be aware of is the -fmls_peak_value in step 12 and the -cutoff value in step 19.
The documentation states a value of 0.06 in both instances. However, this might be too low. In my case, 0.08 was a better choice as 0.06 gave too many spurious fixels/tracts in GM. 0.08 stroke a nice balance in reducing spurious fixels/tracts while retaining crossing fibres in WM.
As always, it is essential to evaluate the quality/validity of each of the processing steps.
See also discussion in post FBA pipeline - quality check for several steps
A nice overview article and associated code can be found here: GitHub - smeisler/Meisler_Reading_FBA: Code used in the Meisler and Gabrieli 2022 eLife paper on fixel based analyses of reading abilities.
Below are some screenshots. (1) FA study template, (2) whole brain tractogram 0.06, (3) tractogram 0.08
Thank you for you reply!
I really appreciate you answer but I think my question wasn’t clear enough!
What I’m trying to have is a template similar to the image attached below.
Is there any parameters that I have to follow or to learn to get such a similar template as in Mito and al.
? or it might be leaded to an intensity problem ?
Because what I’m having unfortunately is a template that shows that the white mater is grey you can see it in my first post.
I hope someone could help me cause it’s been two weeks that I’m trying to figure a solution.
Looking forward for your answers
I think the appearance of the FOD template has to do with differences in b-values, the number of directions and shells in the data you have. At lower b-value and in single shell, the contrast will get the kind of results you are showing (although you can play with the intensity scale by maintaining right click in mrview).
See this previous related thread:
The term “tractogram” is more often used to refer to the 3D tracts from the track files (.tck) William has shown coloured in his 2nd/3rd pictures, I too misunderstood your question at first.
I hope that helps