# Problem with dwi2response msmt\_5tt (amp2response) command for ex-vivo monkey data

**URL:** https://community.mrtrix.org/t/problem-with-dwi2response-msmt-5tt-amp2response-command-for-ex-vivo-monkey-data/1402
**Category:** Uncategorized
**Created:** [January 15, 2018, 2:23pm UTC](https://community.mrtrix.org/t/problem-with-dwi2response-msmt-5tt-amp2response-command-for-ex-vivo-monkey-data/1402 "2018-01-15T14:23:13Z")
**Posts on this page:** 1
**Showing post:** 9

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### 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: [January 17, 2018, 7:29am UTC](https://community.mrtrix.org/t/problem-with-dwi2response-msmt-5tt-amp2response-command-for-ex-vivo-monkey-data/1402/9 "2018-01-17T07:29:05Z")

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> [@jdtournier](#):
>
> In particular, what do the fa.mif and 5tt\_regrid.mif images look like…?

This would be helpful to show us a screenshot of. If doing so, definitely add a colour scale bar to the FA image. Depending on the spatial resolution of your data, I’m not per se surprised that a large number of voxels get selected by that particular algorithm, in particular in an ex-vivo monkey brain (but still it would have to be supported by your spatial resolution).

Unless something that we hadn’t anticipated is wrong with your 5TT image, you may get luckier with the `dhollander` algorithm (if I say so myself 🙄), which doesn’t need a 5TT image. For ex-vivo data you may need to lower the `-fa` parameter, although given your highest b-value being 7000, it may not be necessary after all. See a few posts about this over here:

- [Estimate response function for multi-shell ex-vivo marmoset data - #10 by ThijsDhollander](http://community.mrtrix.org/t/estimate-response-function-for-multi-shell-ex-vivo-marmoset-data/1018/10)
- [Multi-tissue CSD](http://community.mrtrix.org/t/multi-tissue-csd/1268)

But definitely screen shot those FA and 5TT images for us… who knows what we might see.

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