Motion censoring (scrubbing) on CPAC

Software Support
1

Hello everyone,

I’m customizing the default pipeline to preprocess infant data with CPAC and was wondering if it’s possible to include motion censoring (scrubbing) for volumes exceeding a specific FD/DVARS.

Thanks in advance!

2

Hi @luisagulleiro,

This part of the C-PAC documentation has info on specifying FD/DVARS thresholds. Let me know if I can help you with integrating this into your config!

3

Thanks for your help @tamsinrogers! How can this be integrated into the pipeline yml file? Under motion_estimates_and_correction I can’t find an option to specifiy FD thresholds… Should it be included in nuisance_corrections as a custom regressor?

4

Hi @luisagulleiro ,

You can add specifications for each regressor to 2-nuisance_regression in nuisance_corrections:

nuisance_corrections:
  2-nuisance_regression:
    Regressors:
      - Name: {string}
        Censor:
          method: {one of ["Kill", "Zero", "Interpolate", "SpikeRegression"]}
          number_of_previous_trs_to_censor: {int}
          number_of_subsequent_trs_to_censor: {int}
          thresholds: {as many as applicable}
          - type: {one of ['FD_J', 'FD_P', 'DVARS']}
            value: {int}

let me know if that gives you any issues or if I can clarify further!