Work with 'BIDS' (Brain Imaging Data Structure) Projects

Documentation for package ‘bidser’ version 0.5.0

Help Pages

-- A --

anat_parser	Anatomical parser constructor
as_bids_uri	Coerce to a BIDS URI object
as_bids_uri.bids_uri	Coerce to a BIDS URI object
as_bids_uri.character	Coerce to a BIDS URI object

-- B --

bids_check_compliance	Basic BIDS Compliance Checks
bids_datatype_spec	Build a custom BIDS datatype spec
bids_entities	Parse BIDS entities from paths into a tibble
bids_heatmap	Create a specialized heatmap visualization of BIDS data
bids_index	Build or retrieve a persistent file index for a BIDS project
bids_parser	BIDS filename parsers using regex
bids_project	Create a BIDS Project Object
bids_report	Create a lightweight text report for a BIDS project
bids_report_data	Assemble lightweight report data for a BIDS project
bids_schema	Load and cache the BIDS schema
bids_schema_versions	List available BIDS schema versions
bids_subject	Access a single subject from a BIDS project
bids_subject.bids_project	Access a single subject from a BIDS project
bids_summary	Summarize a BIDS dataset
bids_transform	Apply a transformation to BIDS files
bids_uri	Construct a BIDS URI object
bids_version	Get the BIDS version of a dataset
bids_version.bids_dataset_description	Get the BIDS version of a dataset
bids_version.bids_project	Get the BIDS version of a dataset
bids_version.mock_bids_project	Get the BIDS version of a dataset
brain_mask	Retrieve a brain mask for a subject
brain_mask.bids_project	Retrieve a brain mask for a subject
build_subject_graph	Build Subject Graph Structure
build_subject_graph.bids_project	Build Subject Graph Structure
build_subject_graph.mock_bids_project	Build Subject Graph Structure

-- C --

check_confounds	Check and clean confound tables
check_func_scans	Check Functional Scans in a BIDS Project
clean_confounds	Check and clean confound tables
clear_example_bids_cache	Clear Example BIDS Dataset Cache
confound_files	Get confound files from a BIDS project
confound_files.bids_project	Get confound files from a BIDS project
confound_files.mock_bids_project	Get confound files from a BIDS project
confound_set	Convenience confound sets for fMRIPrep
confound_strategy	Confound denoising strategies
create_mock_bids	Create a Mock BIDS Project Object
create_preproc_mask	Create a preprocessing mask from BIDS data
create_preproc_mask.bids_project	Create a binary brain mask from preprocessed scans
create_preproc_mask.mock_bids_project	Create Preprocessing Mask (Mock Implementation)
create_smooth_transformer	Create a simple smoothing transformer

-- D --

dataset_description	Get the dataset_description object from a BIDS project
dataset_description.bids_project	Get the dataset_description object from a BIDS project
dataset_name	Get fields from a BIDS dataset description
dataset_type	Get fields from a BIDS dataset description
decode_bids_entities	Decode BIDS entities back into a filename
derivative_files	Query derivative files from a BIDS project
derivative_pipelines	List derivative pipelines in a BIDS project

-- E --

encode	Encode a string into a BIDS key-value list
encode.character	Encode a string into a BIDS key-value list
event_files	Get event files from a BIDS project
event_files.bids_project	Get event files from a BIDS project
event_files.mock_bids_project	Get event files from a BIDS project

-- F --

file_pairs	Find File Pairs in a BIDS Project
flat_list	Get "flat" representation of BIDS Project
flat_list.bids_project	Get "flat" representation of BIDS Project
fmap_parser	Fieldmap parser constructor
fmriprep_anat_parser	fMRIPrep anatomical parser constructor
fmriprep_func_parser	fMRIPrep functional parser constructor
func_parser	Functional parser constructor
func_scans	Get functional scans from a BIDS project
func_scans.bids_project	Get Functional Scans from a BIDS Project
func_scans.mock_bids_project	Get functional scans from a BIDS project

-- G --

gen_parser	Generate a parser from a spec
get_example_bids_dataset	Download Example BIDS Dataset
get_metadata	Resolve metadata for a BIDS file
get_metadata.bids_project	Resolve metadata for a BIDS file
get_repetition_time	Get Repetition Time (TR) from a sidecar JSON

-- I --

infer_tr	Infer TR (Repetition Time) from a BOLD file or sidecar
infer_tr.character	Infer TR (Repetition Time) from a BOLD file or sidecar
is_bids_uri	Test whether an object is a BIDS URI

-- L --

list_confound_sets	List available confound sets
list_confound_strategies	List available confound strategies
list_datatypes	List registered BIDS datatypes
list_pack_bids	List Contents of Packed BIDS Archive
load_all_events	Load All Event Files
load_all_events.bids_project	Load All Event Files

-- M --

mask_files	Query Mask Files from a BIDS Project
mask_files.bids_project	Query Mask Files from a BIDS Project
mask_files.mock_bids_project	Query Mask Files from a BIDS Project

-- N --

n_volumes	Get the number of volumes in functional scans
n_volumes.bids_project	Get the number of volumes in functional scans
n_volumes.character	Get the number of volumes in functional scans

-- P --

pack_bids	Pack BIDS Project with Stub or Downsampled Imaging Files
parse	Parse a file-name into BIDS components
participants	Get participants from a BIDS project
participants.bids_project	Get participants from a BIDS project
participants.mock_bids_project	Get Participants from Mock BIDS Project
plot.bids_confounds	Plot PCA confounds
plot.bids_project	Plot a BIDS project as a dendrogram
plot.mock_bids_project	Plot a BIDS project as a dendrogram
plot_bids	Plot a comprehensive visual overview of a BIDS project
preproc_scans	Get preprocessed functional MRI scans
preproc_scans.bids_project	Get preprocessed scans from a BIDS project
print.mock_bids_project	Print Mock BIDS Project Summary

-- Q --

query_files	Query files in BIDS structure with explicit semantics
query_files.bids_project	Query files in BIDS structure with explicit semantics
query_files.mock_bids_project	Query files in BIDS structure with explicit semantics

-- R --

read_confounds	Read Confound Files from a BIDS Project
read_confounds.bids_project	Read confound files
read_confounds.mock_bids_project	Read Confound Files (Mock Implementation)
read_dataset_description	Read the dataset_description.json for a BIDS project
read_dataset_description.bids_project	Read the dataset_description.json for a BIDS project
read_dataset_description.character	Read the dataset_description.json for a BIDS project
read_events	Read Event Files from a BIDS Project
read_events.bids_project	Read event files from a BIDS project
read_events.mock_bids_project	Read Event Files from Mock BIDS Project
read_func_scans.bids_project	Read in a set of four-dimensional functional scans
read_participants	Read participants.tsv as a typed tabular object
read_participants.bids_project	Read participants.tsv as a typed tabular object
read_participants.character	Read participants.tsv as a typed tabular object
read_preproc_scans.bids_project	Read preprocessed functional MRI scans from a BIDS project
read_scans_tsv	Read a scans.tsv file for a subject
read_scans_tsv.bids_project	Read a scans.tsv file for a subject
read_sessions_tsv	Read a sessions.tsv file for a subject
read_sessions_tsv.bids_project	Read a sessions.tsv file for a subject
read_sidecar	Read sidecar JSON files and return metadata as a tidy tibble
register_datatype	Register a custom BIDS datatype
resolve_bids_uri	Resolve a BIDS URI to a local or remote path
resolve_bids_uri.bids_uri	Resolve a BIDS URI to a local or remote path
resolve_bids_uri.character	Resolve a BIDS URI to a local or remote path

-- S --

search_files	Search files in BIDS structure
search_files.bids_project	Search files in BIDS structure
search_files.mock_bids_project	Search files in BIDS structure
sessions	Get sessions from a BIDS project
sessions.bids_project	Get sessions from a BIDS project
sessions.mock_bids_project	Get Sessions from Mock BIDS Project
sidecar	Get the sidecar metadata attached to a tabular BIDS object
sidecar.bids_tabular	Get the sidecar metadata attached to a tabular BIDS object
surface_files	Query Surface Files from a BIDS Project
surface_files.bids_project	Query Surface Files from a BIDS Project
surface_files.mock_bids_project	Query Surface Files from a BIDS Project

-- T --

tasks	Get tasks from a BIDS project
tasks.bids_project	Get tasks from a BIDS project
tasks.mock_bids_project	Get Tasks from Mock BIDS Project
transform_files	Query Transform Files from a BIDS Project
transform_files.bids_project	Query Transform Files from a BIDS Project
transform_files.mock_bids_project	Query Transform Files from a BIDS Project

-- U --

unregister_datatype

Unregister a custom BIDS datatype

-- V --

variables_table

Create a tidy run-level variables table