↔️ Fmriprep Ingress

[e-kenneally]

Fixes

Fixes #1902

Description

This new feature offers the ability to ingress fmriprep output data directly into the C-PAC resource pool, so that users can then proceed to perform further processing. Example: pulling in the confounds.tsv and also the BOLD time series that has already been preprocessed and warped to template; then, C-PAC can proceed with denoising and anything else, including calculating connectomes and other derivatives.

Technical details

How to run:

• Select preconfig fmriprep-ingress or modify pipeline_config_fmriprep-ingress.yml if you want to use more regressors
• Add output dir to data config under derivatives_dir
• Data config only needs to contain:
  • Site
  • Subject_id
  • Unique_id
  • Derivatives_dir
• Run command will need something in the $Data field, but this won’t be touched and can be any path

New preconfig: fmriprep-ingress

• Outdir_ingress:
Run: On
Template: MNI152NLin2009cAsym
• The 'template' sub-field is only important when the output directory contains outputs in more than one template space
• Anatomical and functional preprocessing is turned off
• Default regressors:
  • global_signal
  • white_matter
• Derivatives:
  • Time Series extraction with atlas list from default config
  • Alff/fAlff - Template space only
  • ReHo - Template space only
  • Network centrality

Major changes:

• ingress_output_dir function, which is called instead of ingress_raw_anat_data and ingress_raw_func_data. This function pulls in the files from the fmriprep output directory and stores them in the resource pool.
• New preconfig fmriprep-ingress
• Regressors ingress: created a new nodeblock ingress_regressors connected to a pipeline switch that pulls in and parses regressors from the provided output directory. This allows the user to select which regressors they would like to apply to the data.
• Added new function ingress_freesurfer that makes FreeSurfer ingress more modular. FreeSurfer derivatives don't yet run on fMriPrep output directories, but the functionality can be used when ingressing CPAC output directories.

Tests

Correlations for desc-preproc_bold done with pre-configured pipelines:
fmriprep-ingress x fmriprep LTS: 0.65
fmriprep-options x fmriprep LTS: 0.66
fmriprep-ingress x fmriprep-options: 0.41

Correlations for template space desc-bold_mask (called desc-brain_mask in fmriprep):
fmriprep-ingress x fmriprep LTS: 0.978
fmriprep-ingress x fmriprep-options: 0.962

Correlations for derivatives: (ingress derivatives x fmriprep-options derivatives)
- fALFF - 0.92
- ReHo - 0.85
- ALFF - 0.86

Screenshots

Checklist

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• My pull request targets the develop branch of the repository.
• My commit messages follow best practices.
• My code follows the established code style of the repository.
• I added tests for the changes I made (if applicable).
• I updated the changelog.
• I added or updated documentation (if applicable).
• I tried running the project locally and verified that there are no visible errors.

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[sgiavasis]

Great work @e-kenneally !! 🚀

[shnizzedy]

Just want to clarify a couple things if you're ingressing that I noticed when working on #2011:

1. You need to specify Regressors in your pipeline config to match what's in your ingress_regressors?
2. You can only have one named Regressors dict if you're using ingress_regressors?