Skip to contents

Postprocess a single fMRI BOLD image using a configured pipeline

Source: R/postprocess_subject.R
postprocess_subject.Rd

Applies a sequence of postprocessing operations to a single subject-level BOLD NIfTI file, as specified by the user-defined configuration object. Operations may include brain masking, spatial smoothing, ICA-AROMA denoising, temporal filtering, confound regression, and intensity normalization. The function also optionally computes and saves a filtered confounds file for downstream analyses.

Usage

postprocess_subject(in_file, cfg = NULL)

Arguments

in_file

Path to a subject-level BOLD NIfTI file output by fMRIPrep.

cfg

A list containing configuration options, including TR (cfg$tr), enabled processing steps (cfg$<step>$enable), logging (cfg$log_file), and paths to resources such as singularity images (cfg$fsl_img). A whole-brain mask is automatically generated using automask() and used for relevant processing steps.

Value

The path to the final postprocessed BOLD NIfTI file. Side effects include writing a confounds TSV file (if enabled), and logging to a subject-level log file.

Details

The processing sequence can be enforced by the user (force_processing_order = TRUE) or determined dynamically based on the enable flags in the configuration. Intermediate NIfTI and confound files are staged inside a scratch workspace (located under cfg$scratch_directory) and final outputs are written or moved into the postprocessing output directory. Logging is handled via the lgr package and is directed to subject-specific log files inferred from BIDS metadata.

Required cfg entries:

  • tr: Repetition time in seconds.

  • bids_desc: A BIDS-compliant desc label for the output filename.

  • processing_steps: Optional character vector specifying processing order (if force_processing_order = TRUE).

  • scratch_directory: Optional directory for staging intermediate files (defaults to tempdir() if unset).

  • project_name: Optional project label used to organize scratch workspaces.

Optional steps controlled by cfg$<step>$enable:

  • apply_mask

  • spatial_smooth

  • apply_aroma

  • temporal_filter

  • confound_regression

  • intensity_normalize