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

**URL:** <https://community.mrtrix.org/t/questions-about-fod-abnormalities-and-bias-correction-in-single-shell-fba-pipeline/8414>\
**Category:** Uncategorized\
**Created:** [June 22, 2025, 8:48am UTC](https://community.mrtrix.org/t/questions-about-fod-abnormalities-and-bias-correction-in-single-shell-fba-pipeline/8414 "2025-06-22T08:48:53Z")\
**Posts on this page:** 1\
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**Author:** ![WilliamFCB](https://community.mrtrix.org/letter_avatar_proxy/v4/letter/w/e68b1a/32.png) [@WilliamFCB](https://community.mrtrix.org/u/WilliamFCB)\
**Post date:** [June 23, 2025, 6:55am UTC](https://community.mrtrix.org/t/questions-about-fod-abnormalities-and-bias-correction-in-single-shell-fba-pipeline/8414/2 "2025-06-23T06:55:01Z")

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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](https://github.com/PennLINC/qsiprep), 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](https://www.nature.com/articles/s41597-022-01695-7))

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

> **[Meisler\_Reading\_FBA/fba/bash\_scripts at main · smeisler/Meisler\_Reading\_FBA](https://github.com/smeisler/Meisler_Reading_FBA/tree/main/fba/bash_scripts)**
>
> Code used in the Meisler and Gabrieli 2022 eLife paper on fixel based analyses of reading abilities. - smeisler/Meisler\_Reading\_FBA

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

In the case of masks: synthstrip: [synthstrip.io](https://surfer.nmr.mgh.harvard.edu/docs/synthstrip). 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](https://3tissue.github.io/doc/ss3t-csd.html), is the recommended algorithm (see discussion: [Single shell vs. "Single tissue" - #5 by araikes](https://community.mrtrix.org/t/single-shell-vs-single-tissue/5761/5))

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](https://community.mrtrix.org/t/fba-pipeline-quality-check-for-several-steps/5747)). Anyway, as recommended in the guidelines, it is best to check this on your own data.

Cheers  
William

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