API

bidsaid.audit

Module for auditing directories.

BIDSAuditor

Check availability of different files for each subject in the BIDS directory.

bidsaid.files

Module for initializing and creating BIDS compliant files.

generate_bids_filename	Generate a BIDs compliant filename.
create_bids_file	Create a BIDS compliant filename with required and optional entities.
get_entity_value	Gets entity value of a BIDS compliant filename.
create_dataset_description	Generate a dataset description dictionary.
save_dataset_description	Save a dataset description dictionary.
create_participant_tsv	Creates a basic dataframe for the "participants.tsv" file.
create_sessions_tsv	Creates a basic dataframe for the "sub-{subject_ID}_sessions.tsv" file for a specific subject.

bidsaid.events

Module containing classes for extracting timing information from Presentation and E-Prime logs.

PresentationBlockExtractor	Extract onsets, durations, and trial types from Presentation logs using a block design.
PresentationEventExtractor	Extract onsets, durations, trial types, reaction times, and responses from Presentation logs using an event design.
EPrimeBlockExtractor	Extract onsets, durations, and trial types from E-Prime logs using a block design.
EPrimeEventExtractor	Extract onsets, durations, trial types, reaction times, and responses from E-Prime logs using an event design.

bidsaid.logging

Module setting up a logger.

setup_logger

Sets up the logger.

bidsaid.io

Module for input/output operations on NIfTI files and images.

load_nifti	Loads a NIfTI image.
compress_image	Compresses a ".nii" image to a ".nii.gz" image.
is_nifti_truncated	Checks expected byte size and actual byte size of uncompressed NIfTI images.
regex_glob	Use regex to get content in the source directory with specific patterns.
get_nifti_header	Get header from a NIfTI image.
get_nifti_affine	Get the affine matrix from a NIfTI image.
replace_ext	Replaces extension of a filename.

bidsaid.path_utils

Utilities related to parsing or sorting filenames.

is_valid_date	Determine if a string is a valid date based on format.
parse_date_from_path	Get date from the stem of a path.
get_file_timestamp	Get timestamp of file.
get_file_creation_date	Get creation date of a file
sort_by_acquisition_order	Sort filenames based on acquisition sequence.

bidsaid.metadata

Module containing functions to extract metadata information from NIfTIs.

needs_resampling	Determines if a source image needs to be resampled.
determine_slice_axis	Determine the slice axis.
get_hdr_metadata	Get metadata from a NIfTI header.
get_n_volumes	Get the number of volumes from a 4D NIftI image.
get_image_orientation	Get the image orientation.
direction_to_voxel_axis	Returns the voxel coordinate axis (and position) of a given anatomical direction.
get_n_slices	Gets the number of slices from the header of a NIfTI image.
get_tr	Get the repetition time from the header of a NIfTI image.
create_slice_timing	Create slice timing dictionary mapping the slice index to its acquisition time.
is_3d_img	Determines if nifti_file_or_img is a 3D image.
get_scanner_info	Determines the manufacturer and model name of scanner.
infer_task_from_image	Infer the task based on the number of volumes in a 4D NIfTI image.
get_recon_matrix_pe	Get the reconstruction matrix of the phase encoding axis.
compute_effective_echo_spacing	Compute the effective echo spacing for Philips 3T MRI.
compute_total_readout_time	Compute the total readout time.

bidsaid.parsers

Module containing functions to parse raw logs from stimulus Presentation and E-Prime 3 software.

convert_edat3_to_text	Converts a file with an "edat3" extension to a text file.
load_eprime_log	Loads E-Prime 3 log file as a Pandas Dataframe.
load_presentation_log	Loads Presentation log file as a Pandas DataFrame.
get_presentation_log_date	Gets the date and time from a Presentation logfile.

bidsaid.qc

Module for quality control metrics and assessment of fMRI data.

compute_n_dummy_scans	Compute the number of dummy scans based on the number of "non_steady_state_outlier_XX" columns in an fMRIPrep confounds TSV file.
compute_framewise_displacement	Computes the framewise displacement using the Power (2012) formula:
create_censor_mask	Create a censor mask where 0 indicates volumes to censor and 1 indicates volumes to keep.
merge_censor_masks	Merge multiple censor masks.
compute_consecutive_censor_stats	Compute the mean and standard deviation of the consecutive censored volumes.
create_spike_regressors	Creates spike regressors that can be used to censor certain frames during regression.
get_n_censored_volumes	Computes number of censored volumes.
compute_global_signal	Compute global signal and percent signal change from functional NIfTI image.

bidsaid.simulate

Module for simulating NIfTI images and BIDS datasets.

simulate_nifti_image	Simulates a NIfTI image with random data within the MNI152 brain template.
simulate_bids_dataset	Generate a Simulated BIDS Dataset with fMRIPrep Derivatives.