# Fixel-Based Analysis on single shell data **URL:** \ **Category:** Uncategorized\ **Tags:** fba\ **Created:** [May 17, 2017, 12:33am UTC](https://community.mrtrix.org/t/fixel-based-analysis-on-single-shell-data/897 "2017-05-17T00:33:09Z")\ **Posts on this page:** 1\ **Showing post:** 8
**Author:** ![ThijsDhollander](https://community.mrtrix.org/user_avatar/community.mrtrix.org/thijsdhollander/32/1617_2.png) [@ThijsDhollander](https://community.mrtrix.org/u/ThijsDhollander)\ **Post date:** [August 17, 2017, 5:17am UTC](https://community.mrtrix.org/t/fixel-based-analysis-on-single-shell-data/897/8 "2017-08-17T05:17:55Z")
Just a small addition here: as I’ve mentioned in [this post](https://community.mrtrix.org/t/error-using-mtnormalise/1111/5) just now, you can actually also continue using the multi-tissue pipeline after you’ve obtained the WM and CSF outcomes from `dwi2fod msmt_csd`. So essentially still `dwi2response dhollander`, ditching the GM response, `dwi2fod msmt_csd` with only WM and CSF responses, but then _not_ ditching the CSF outcome, but proceeding with the **multi-tissue pipeline** (rather than the single-shell one) while using 2 tissue types (rather than the exemplary 3 in the documentation). The `mtnormalise` step should work quite well with WM and CSF, as long as they come from an actual 2-tissue WM-CSF reconstruction (so _not_ from a 3-tissue WM-GM-CSF reconstruction where you ditch the GM; that would be ditching actual signal, which isn’t good for `mtnormalise`). The reason why this still works very decently, is because the b=0 signal from GM is still not _massively_ different from WM, and the non-b=0 signal will in most scenarios be the other way around. The CSF compartment will also still fit a tiny bit of the actual GM. So putting this all together, the summed WM+CSF image from a WM+CSF 2-tissue reconstruction, plus rebalancing (which `mtnormalise` does internally for you), still results in a quite flat image; apart from T2 shine-through and bias fields. That’s exactly the assumption that `mtnormalise` hinges on, so it does perform well in practice. --- _[View the full topic](https://community.mrtrix.org/t/fixel-based-analysis-on-single-shell-data/897)._