Package index • BrainGnomes

All functions

add_tracked_job_parent(): Add parent/child id relationship to tracking database
automask(): Create an automatic brain mask from a NIfTI image (Rcpp implementation)
butterworth_filter_4d(): Apply a Butterworth Filter to a 4D NIfTI Image
calculate_motion_outliers(): Summarize framewise displacement outliers across runs
cancel_project_run(): Cancel queued or running jobs from one run
cluster_job_submit(): This function submits a single script to a high-performance cluster using a scheduler (Slurm or TORQUE). It accepts a vector of arguments to be passed to the scheduler and a vector of environment variables that should be passed to the compute node at job execution.
construct_bids_filename(): Construct BIDS-Compatible Filenames from Extracted Entity Data
construct_bids_regex(): Construct a Regular Expression for Matching BIDS Filenames
derive_reference_core(): Derive a conservative functional reference core from 4D BOLD data
diagnose_pipeline(): Deprecated interactive pipeline diagnosis
diagnose_project(): Diagnose failed project work
doctor(): Project preflight shorthand
doctor_project(): Run non-mutating project and runtime preflight checks
edit_project(): Interactively edit a project configuration by field (field-guided)
extract_bids_info(): Extract fields from BIDS filenames
extract_rois(): Extract ROI timeseries and connectivity matrices
filtfilt_cpp(): Zero-Phase IIR Filtering via Forward and Reverse Filtering
find_run_logs(): Find output and error logs for one run
get_fmriprep_outputs(): Identify fMRIPrep-Derived Outputs for a NIfTI File
get_postproc_output_files(): List postprocessed output files for paired input specifications
get_project_runs(): List submitted runs for a project
get_project_status(): Get processing status for all subjects
get_run_jobs(): Inspect the jobs submitted for one project run
get_run_provenance(): Read the complete provenance record for a project run
get_subject_status(): Get processing status for a single subject
get_tracked_job_status(): Query job status in tracking SQLite database
getline(): Read a Line of Input from the User in Both Interactive and Non-Interactive Sessions
image_quantile(): Compute Quantiles from a 3D or 4D NIfTI Image
initialize_project(): Initialize a BrainGnomes project interactively or from portable defaults
insert_df_sqlite(): helper function to insert a keyed data.frame into the sqlite storage database
insert_tracked_job(): Internal helper function to insert a job into the tracking SQLite database
inspect_project(): Inspect current project progress
lmfit_residuals_4d(): Apply Confound Regression to 4D fMRI Data Using Voxelwise Linear Models
load_project(): Load a project configuration from a file
natural_spline_4d(): Interpolate fMRI Time Series with Cubic Splines in a NIfTI File
natural_spline_interp(): Cubic spline interpolation with natural spline and linear extrapolation
parse_cli_args(): Parse CLI-style arguments into a nested list using args_to_df()
plan_project(): Inspect or persist the resolved project execution model
postprocess_subject(): Postprocess a single fMRI BOLD image using a configured pipeline
read_project_plan(): Read a saved execution plan
remove_nifti_volumes(): Remove Specified Timepoints from a 4D NIfTI Image
resample_template_to_img(): Resample TemplateFlow Mask to fMRIPrep Image Using Python
retry_project_run(): Create a new run for failed work
run_bids_validation(): Run BIDS validation on the project BIDS directory
run_fsl_command(): Run an FSL command with optional Singularity container support and structured logging
run_project(): Run the processing pipeline
setup_project(): Setup the processing pipeline for a new fMRI study
submit_project_plan(): Submit a saved or in-memory execution plan
summary(<bg_project_cfg>): summary method for project configuration object
summary(<bg_status_df>): Summarize project status
update_tracked_job_status(): Update Job Status in Tracking SQLite Database
validate_project_config(): Validate a BrainGnomes project configuration without changing it
wait_for_job(): This function pauses execution of an R script while a scheduled qsub job is not yet complete.
write_project_config(): Write a project configuration without interactive prompts
write_project_plan(): Save an execution plan to YAML