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

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

## Documentation for package ‘bidser’ version 0.2.0

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

## Help Pages

anat_parser | Anatomical parser constructor
bids_check_compliance | Basic BIDS Compliance Checks
bids_heatmap | Create a specialized heatmap visualization of BIDS data
bids_parser | BIDS filename parsers using regex
bids_project | Create a BIDS Project Object
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
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
check_func_scans | Check Functional Scans in a BIDS Project
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
decode_bids_entities | Decode BIDS entities back into a filename
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
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
get_example_bids_dataset | Download Example BIDS Dataset
get_repetition_time | Get Repetition Time (TR) from a sidecar JSON
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
list_confound_sets | List available confound sets
list_confound_strategies | List available confound strategies
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
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
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
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_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_preproc_scans.bids_project | Read preprocessed functional MRI scans from a BIDS project
read_sidecar | Read sidecar JSON files and return metadata as a tidy tibble
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
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
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