Questions about FOD abnormalities and bias correction in single-shell FBA pipeline

1

Dear MRtrix3 community,

I’m implementing a Fixel-Based Analysis pipeline using single-shell DTI data (1 b=0, 55 b=1000). I have three questions regarding intermediate results:

Response functions validation
The response functions generated by dwi2response dhollander show expected patterns (WM anisotropic, GM/CSF isotropic). Example WM response:

3195.43787503105 0 0 0 0 0
1667.16418134566 -647.345954963735 141.155732127141 -26.0966573674176 1.46582648483342 0.0495213266841901
Is this format correct for single-shell data? shview shows the expected shapes.

Abnormal FOD distributions
After dwi2fod msmt_csd:

    GM FODs show no FOD in cortical areas (screenshot attached)
    WM FODs display fiber orientations in grey matter regions



    Population template (group_wm_fod_template.mif) shows FOD lobes extending into GM

grey matter regions in group white matter FOD template
grey matter regions in group white matter FOD template1920×1269 649 KB

    Is this expected behavior for b=1000 data? Could this be due to:
    a) Limited GM/WM differentiation at low b-values?
    b) Contamination in GM response estimation?
    c) Fundamental limitations of MSMT-CSD with single-shell data?

Bias correction necessity
While dwibiascorrect ants is recommended, some suggest it may introduce artifacts. How should we evaluate:
a) When is it safe to omit this step?
b) Are there quantitative metrics to validate correction effectiveness?
c) Does correction affect fixel metrics (FD/FC/FDC) differently?

Data specifics:
Scanner: 3T GE MR Discovery
Resolution: 112mm
Preprocessing: Denoising, Gibbs unringing, Eddy correction, Bias correction and Global intensity normalisation

2

Hi Xiaodong,

I am not an expert, but in case you don’t have this information already, I’ve included some suggestions and details that may be of use.

I typically and successfully use QSIprep for the DWI preprocessing (including bias correction) (GitHub - PennLINC/qsiprep: Preprocessing of diffusion MRI, which also generates some QC measures (see also their article on this: An analysis-ready and quality controlled resource for pediatric brain white-matter research | Scientific Data)

Besides the Mrtrix documentation, a good resource, with scripts, for FBA is:

Of course, there is the paper:
https://www.sciencedirect.com/science/article/pii/S1053811921006923?via%3Dihub

In the case of masks: synthstrip: synthstrip.io. Also part of Freesurfer is a very versatile tool.

Importantly, note that for “Single” data, the Single-Shell 3-Tissue CSD (SS3T-CSD) and not MSMT-CSD: Single-Shell 3-Tissue CSD (SS3T-CSD) | MRtrix3Tissue, is the recommended algorithm (see discussion: Single shell vs. "Single tissue" - #5 by araikes)

Finally, while the documentation states a threshold (e.g., -fmls_peak_value) of 0.6, 0.8 might be a better choice in many cases (see: Dhollander (FBA pipeline - quality check for several steps). Anyway, as recommended in the guidelines, it is best to check this on your own data.

Cheers
William