# Single shell DTI-data
**URL:** https://community.mrtrix.org/t/single-shell-dti-data/4468
**Category:** Uncategorized
**Created:** [January 14, 2021, 10:12am UTC](https://community.mrtrix.org/t/single-shell-dti-data/4468 "2021-01-14T10:12:53Z")
**Posts on this page:** 4
**Page:** 1
### Author:  [@Jolie](https://community.mrtrix.org/u/Jolie)
#### Post date: [January 14, 2021, 10:12am UTC](https://community.mrtrix.org/t/single-shell-dti-data/4468/1 "2021-01-14T10:12:54Z")
Hello
Any good advice for analysis of single shell DTI-data (I’ve got b0 and b1000). I’ve done the preprocessing (dwifslpreproc and masking). Should I go back to FSL, or is there a pipeline through MRTrix? I’m interested in both WM and GM, and ROI- analysis is of interest. I’ve enjoyed the BATMAN-tutorial, but since I don’t have multishell data, I have to find a new way as I’ve understood it.
New to the game, so any clues or good advice are welcome and appreciated!
Cheers!
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### Author:  [@ChrisvdW](https://community.mrtrix.org/u/ChrisvdW)
#### Post date: [January 14, 2021, 10:56am UTC](https://community.mrtrix.org/t/single-shell-dti-data/4468/2 "2021-01-14T10:56:02Z")
I guess, that depends kinda on what you want to achieve. If you want to derive DTI parameters, like FA, MD, RD, AD, you can chose to do that with FSL or MRtrix. The main advantage of using MRtrix, is in my opinion, the ease of several tools integrated in the pipeline (including FSL).
Basically, I would follow this tutorial till step 4 (thus stop after step 3, the bias field correction), and then perform dwi2tensor.
> **[Fibre density and cross-section - Multi-tissue CSD — MRtrix 3.0 documentation](https://mrtrix.readthedocs.io/en/latest/fixel_based_analysis/mt_fibre_density_cross-section.html)**
Thus in order:
1. dwidenoise
2. mrdegibbs
3. dwifslpreproc
4. dwibiascorrect ants
5. dwi2tensor (or you can switch to FSL and run dtifit)
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### Author:  [@jdtournier](https://community.mrtrix.org/u/jdtournier)
#### Post date: [January 14, 2021, 12:14pm UTC](https://community.mrtrix.org/t/single-shell-dti-data/4468/3 "2021-01-14T12:14:56Z")
There is actually a [page on the documentation about using single-shell data](https://mrtrix.readthedocs.io/en/latest/fixel_based_analysis/st_fibre_density_cross-section.html). However, you can do better than this these days, since even single-shell data effectively contains 2 shells: the _b_=0 volumes qualify as a ‘shell’ in this context (we need to update the docs to reflect that… 😳). So you should be able to use your data in more or less exactly the same way as outlined in the BATMAN tutorial, with the only change being the `dwi2fod` call, as [outlined in this post](https://community.mrtrix.org/t/fba-single-shell-high-gm-fod-values/1746/3) and [referred to in this post](https://community.mrtrix.org/t/dwi2fod-with-fa-as-mask/2614/5).
Also: bear in mind that the original CSD method was developed for single-shell data, and is still usable here. It’s not as clean as what you can get with the recommendations above though, but it is nonetheless an option (invoke with `dwi2fod csd`).
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### Author:  [@Jolie](https://community.mrtrix.org/u/Jolie)
#### Post date: [January 20, 2021, 8:26am UTC](https://community.mrtrix.org/t/single-shell-dti-data/4468/4 "2021-01-20T08:26:14Z")
Thank you 🙂