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

## Documentation for package ‘bidser’ version 0.5.0

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS
- Package README

## Help Pages

A B C D E F G I L M N P Q R S T U V

## -- 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