:bug: Enable alff to run without nuisance

[e-kenneally]

Fixes

Description

The current alff/fAlff workflow is set up so that if nuisance regression is in native space and alff is in template space, CPAC runs a nodeblock called warp_denoiseNofilt_to_T1template.

From cpac_pipeline.py:

From registration.py:

This nodeblock requires a file from nuisance regression (desc-denoisedNofilt_bold), so it crashes if nuisance regression is not enabled. Since we don't want alff and nuisance regression to be inter-dependent, I moved the transform nodes from their separate transform nodeblock into the template-space alff nodeblock. Now the transform step gets triggered only if desc-denoisedNofilt_bold is in the strat_pool.

Tests

I successfully ran fmriprep ingress + alff with and without nuisance regression.

Checklist

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Developer Certificate of Origin

Developer Certificate of Origin

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[e-kenneally]

Is it true that desc-denoisedNofilt_bold only exists if 'Template' in target_space_alff and 'Native' in target_space_nuis, or is just checking for the existence desc-denoisedNofilt_bold a better condition for what we care about here?

desc-denoisedNofilt_bold only exists if nuisance regression is running (in native or template space). I made that the check because regardless of the space for nuisance regression, if the file isn't being produced then the template space transform step can't run.

[shnizzedy]

desc-denoisedNofilt_bold only exists if nuisance regression is running (in native or template space). I made that the check because regardless of the space for nuisance regression, if the file isn't being produced then the template space transform step can't run.

Makes sense. I was just wondering if desc-denoisedNofilt_bold will exist / we need to apply the transform if nuisance and ALFF are both in the same space?

[e-kenneally]

Makes sense. I was just wondering if desc-denoisedNofilt_bold will exist / we need to apply the transform if nuisance and ALFF are both in the same space?

Ohh I see! There's a template space version of that file too, so if nuisance runs in template space this won't be triggered. The transform is now only within the template space alff nodeblock, so the conditions that would trigger the transform step are still native nuisance + template alff