ACT in average response functions pipelines

1

Hi all,
I’ve previously tested the pipelines mrtrix_multishell_msmt_noACT_estimate and mrtrix_multishell_msmt_noACT_apply. Is there a reason why there is no ACT in these pipelines. I’m curious because I want to be able to use ACT, but I didn’t know if there is a reason I shouldn’t in this case.

If it’s okay to use ACT, what would the yaml file look like? And is it correct that we would only need to change the “apply” part (instead of “estimate”)?

Best,

Sofie

2

Hi @scchung,

No reason; you can use ACT if you want.

Yes, it would only be applicable for the _apply stage (since it is a tractography argument).

Borrowing from a relevant pipeline ( qsirecon/qsirecon/data/pipelines/mrtrix_multishell_msmt_ACT-hsvs.yaml at main · PennLINC/qsirecon · GitHub ), you would need (assuming you are doing HSVS for your 5TT):

anatomical:
- mrtrix_5tt_hsvs

at the top, and

method_5tt: hsvs

and

use_5tt: true

as parameters to your action: tractography node.

Best,

Steven

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3

Hi @Steven ,
This is great, thank you. If I wanted to use FAST instead, what would the changes be?

Best,

Sofie

4

Hi @scchung ,

We don’t recommend using FAST, but then you would just borrow the anatomical information from another relevant workflow (e.g., qsirecon/qsirecon/data/pipelines/mrtrix_multishell_msmt_ACT-fast.yaml at main · PennLINC/qsirecon · GitHub ):

anatomical:
- mrtrix_5tt_fast

and in tractography parameters:

method_5tt: fast

Best,

Steven

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