# ACT and no reversed phase-encoding information **URL:** \ **Category:** Uncategorized\ **Created:** [August 21, 2017, 4:20am UTC](https://community.mrtrix.org/t/act-and-no-reversed-phase-encoding-information/1122 "2017-08-21T04:20:12Z")\ **Posts on this page:** 6\ **Page:** 1
**Author:** ![mccolgan](https://community.mrtrix.org/user_avatar/community.mrtrix.org/mccolgan/32/1851_2.png) [@mccolgan](https://community.mrtrix.org/u/mccolgan)\ **Post date:** [August 21, 2017, 4:20am UTC](https://community.mrtrix.org/t/act-and-no-reversed-phase-encoding-information/1122/1 "2017-08-21T04:20:12Z")
Dear experts, Apologiies for posting this again, I think it may have been missed the first time round. I am working with multishell data with no reversed phase-encoding information, therefore cannot perform fsl topup. Is it still okay for me to use ACT in this instance? (I note there was some mention of this on the afdconnectivity page). Thanks Peter ---
**Author:** ![rsmith](https://community.mrtrix.org/user_avatar/community.mrtrix.org/rsmith/32/2672_2.png) [@rsmith](https://community.mrtrix.org/u/rsmith)\ **Post date:** [August 23, 2017, 7:49am UTC](https://community.mrtrix.org/t/act-and-no-reversed-phase-encoding-information/1122/2 "2017-08-23T07:49:06Z")
Hi Peter, There’s a brief mention in the [ACT documentation page](http://mrtrix.readthedocs.io/en/latest/quantitative_structural_connectivity/act.html#dwi-distortion-correction), as well as the `afdconnectivity` page as you mentioned; but the better reference would probably be the ACT paper itself. The fundamental assumption underlying ACT is that for any position in space, one can access both orientation information from the DWIs / diffusion model, and tissue information from segmentation of an anatomical image, and that this information corresponds to the _same anatomical location_. If the DWI EPI distortions are not corrected, this assumption can be grossly incorrect. So no, it’s generally advised against using ACT in this instance. Although `tckgen` won’t miraculously crash outright if it detects that your data have not been corrected by `topup`, using ACT may give a false perception of the accuracy of the resulting tracks, and could introduce errors that would not have been there if ACT were omitted. Cheers Rob ---
**Author:** ![mccolgan](https://community.mrtrix.org/user_avatar/community.mrtrix.org/mccolgan/32/1851_2.png) [@mccolgan](https://community.mrtrix.org/u/mccolgan)\ **Post date:** [August 24, 2017, 3:42pm UTC](https://community.mrtrix.org/t/act-and-no-reversed-phase-encoding-information/1122/3 "2017-08-24T15:42:35Z")
Thanks Rob, In that case for the following commands would you be able to recommend alternatives to using 5tt and it’s outputs? # Generate response functions dwi2response msmt\_5tt DWI.mif 5tt.mif RF\_WM.txt RF\_GM.txt RF\_CSF.txt -force # create fod - use if running whole brain tractography dwi2fod msmt\_csd DWI.mif RF\_WM.txt WM\_FODs.mif RF\_GM.txt GM.mif RF\_CSF.txt CSF.mif -mask nodif\_brain\_mask.nii -force #Mask for seeding 5tt2gmwmi 5tt.mif gmwmi.mif -force # Run whole brain tractography - select to retain 5 million tracts sufficient if using sift2 (10M ideal but takes years - could consider for smaller studies tckgen WM\_FODs.mif tracks.tck -act 5tt.mif -backtrack -crop\_at\_gmwmi -seed\_gmwmi gmwmi.mif -select 5M -force Thanks so much for your help. bw Peter ---
**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 24, 2017, 11:27pm UTC](https://community.mrtrix.org/t/act-and-no-reversed-phase-encoding-information/1122/4 "2017-08-24T23:27:43Z")
> [@mccolgan](#): > > Generate response functions > dwi2response msmt\_5tt DWI.mif 5tt.mif RF\_WM.txt RF\_GM.txt RF\_CSF.txt -force That’s an easy one: use ```auto dwi2response dhollander DWI.mif RF_WM.txt RF_GM.txt RF_CSF.txt -force ``` instead. It’s already more accurate out of the box, even on highly corrected incredible quality HCP data ([see, among others, this post](http://community.mrtrix.org/t/dwi2response-dhollander-questions/1095/5)), but if you’re facing a scenario where you’ve got no phase-encoding information, this becomes even more of a no-brainer. I’ve seen `msmt_5tt` response function outcomes in such scenarios before, and it’s not pretty. ---
**Author:** ![mccolgan](https://community.mrtrix.org/user_avatar/community.mrtrix.org/mccolgan/32/1851_2.png) [@mccolgan](https://community.mrtrix.org/u/mccolgan)\ **Post date:** [August 30, 2017, 5:24am UTC](https://community.mrtrix.org/t/act-and-no-reversed-phase-encoding-information/1122/5 "2017-08-30T05:24:45Z")
Thanks this works perfect! Is this okay to use for single shell data as well? I am also using mouse data for another experiment, is this okay for mouse dwi images? Thanks again Peter ---
**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:** [October 28, 2017, 7:45am UTC](https://community.mrtrix.org/t/act-and-no-reversed-phase-encoding-information/1122/6 "2017-10-28T07:45:32Z")
> [@mccolgan](#): > > Is this okay to use for single shell data as well? Yep, no worries. But MSMT-CSD will be limited to 2 tissue types. To get 3 tissue types from such data, you’d need SS3T-CSD, which isn’t available publicly yet. > [@mccolgan](#): > > I am also using mouse data for another experiment, is this okay for mouse dwi images? Sure, no worries again, but you may want to use the `-fa` option to `dwi2response dhollander`, and provide it with a slightly lower value than the default of 0.2. See this post, where success was shown on rat data: [Multi-tissue CSD](http://community.mrtrix.org/t/multi-tissue-csd/1268) . The general advise for a mouse would be similar, but you’d probably have to be extra-careful about setting that parameter decently. Set it to a couple of values, and look at the `-voxels` output to see what makes sense (or doesn’t).