🐛 Possibly safer to use -ort in 3dTProject for SpikeRegression instead

[sgiavasis]

Describe the bug

The nuisance denoising workflow currently uses AFNI 3dTProject's -censor options/sub-options for providing the binary spike regressor. This can lead to inadvertent censoring or scrubbing if not configured properly.

To reproduce

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Preconfig

• default
• abcd-options
• anat-only
• blank
• ccs-options
• fmriprep-options
• fx-options
• monkey
• monkey-ABCD
• ndmg
• nhp-macaque
• preproc
• rbc-options
• rodent

Custom pipeline configuration

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Run command

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Expected behavior

Using the -ort flag to provide the spike regressor vector (.1D file) may be better. Validation needed to ensure the linear regression of the spikes happened correctly.

Acceptance criteria

• No loss of TRs/timepoints.
• Spikes that meet the configured motion threshold are modeled to have their mean removed from the model. (No interpolation or zeroing).

Screenshots

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C-PAC version

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Container platform

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Docker and/or Singularity version(s)

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Additional context

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