Postprocess a single fMRI BOLD image using a configured pipeline

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 brain masks or singularity images (cfg$fsl_img, cfg$brain_mask).

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 may be deleted to save disk space, depending on the keep_intermediates setting. 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).

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

apply_mask
spatial_smooth
apply_aroma
temporal_filter
confound_regression
intensity_normalize