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

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

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

get_fmriprep_outputs(): Identify fMRIPrep-Derived Outputs for a NIfTI File

get_postproc_stream_outputs(): Determine expected output files for a postprocessing stream

get_project_status(): Get processing status for all subjects

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

insert_df_sqlite(): helper function to insert a keyed data.frame into the sqlite storage database

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()

postprocess_subject(): Postprocess a single fMRI BOLD image using a configured pipeline

remove_nifti_volumes: Remove Specified Timepoints from a 4D NIfTI Image

resample_template_to_img(): Resample TemplateFlow Mask to fMRIPrep Image Using Python

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

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

wait_for_job(): This function pauses execution of an R script while a scheduled qsub job is not yet complete.