BIDS-Aid

A toolkit for creating and managing BIDS-compliant fMRI datasets without original DICOMs. Intended for cases that require custom code and flexibility, such as when NIfTI source files lack consistent naming conventions, organized folder hierarchies, or sidecar metadata. Includes utilities for metadata reconstruction from NIfTI headers, file renaming, neurobehavioral log parsing (for E-Prime and Presentation), JSON sidecar generation, surface projection, and making surface clips/movies.

Installation

Standard Installation

pip install bidsaid[all]

Surface projection and movie writing are optional extras: bidsaid[surface] (neuromaps for the fsaverage surfaces), bidsaid[visual] (pyvista for rendering) and bidsaid[movie] (imageio with ffmpeg for writing movies). bidsaid[all] includes everything.

Development Version

git clone --depth 1 https://github.com/donishadsmith/bidsaid/
cd bidsaid
pip install -e .[all]

Features

• File renaming: Convert arbitrary filenames to BIDS-compliant naming

• File creation: Generate dataset_description.json and participants.tsv

• Metadata utilities: Extract header metadata (e.g., TR, orientation, scanner info) and generate slice timing for singleband and multiband acquisitions

• Log parsing: Load Presentation (e.g., .log) and E-Prime 3 (e.g, .edat3, .txt) files as DataFrames, or use extractor classes to generate BIDS events for block and event designs:

  Class	Software	Design	Description
  PresentationBlockExtractor	Presentation	Block	Extracts block-level timing with mean RT and accuracy
  PresentationEventExtractor	Presentation	Event	Extracts trial-level timing with individual responses
  EPrimeBlockExtractor	E-Prime 3	Block	Extracts block-level timing with mean RT and accuracy
  EPrimeEventExtractor	E-Prime 3	Event	Extracts trial-level timing with individual responses

• Auditing: Generate a table showing the presence or absence of certain files for each subject and session

• QC: Creation and computation of certain quality control metrics (e.g., framewise displacement), censoring and temporal interpolation

• Surface movies: Project denoised runs onto the fsaverage surfaces and write per-participant, per-task or group movies with SurfaceRenderer and MovieWriter

Quick Start

Creating BIDS-Compliant Filenames

from bidsaid.files import create_bids_file

create_bids_file(
    src_file="101_mprage.nii.gz",
    sub_id="101",
    ses_id="01",
    desc="T1w",
    dst_dir="/data/bids/sub-101/ses-01/anat",
)

Extracting Metadata from NIfTI Headers

from bidsaid.metadata import get_tr, create_slice_timing, get_image_orientation

tr = get_tr("sub-01_bold.nii.gz")
slice_timing = create_slice_timing(
    "sub-01_bold.nii.gz",
    slice_acquisition_method="interleaved",
    multiband_factor=4,
)
orientation_map, orientation = get_image_orientation("sub-01_bold.nii.gz")

Loading Raw Log Files

from bidsaid.parsers import (
    load_presentation_log,
    load_eprime_log,
    convert_edat3_to_text,
)

presentation_df = load_presentation_log("sub-01_task.log", convert_to_seconds=["Time"])

# E-Prime 3: convert .edat3 to text first, or load .txt directly
eprime_txt_path = convert_edat3_to_text("sub-01_task.edat3")
eprime_df = load_eprime_log(eprime_txt_path, convert_to_seconds=["Stimulus.OnsetTime"])

Creating BIDS Events from Presentation Logs

from bidsaid.events import PresentationBlockExtractor
import pandas as pd

extractor = PresentationBlockExtractor(
    "sub-01_task-faces.log",
    trial_types=("Face", "Place"),  # Can use regex ("Fa.*", "Pla.*")
    scanner_event_type="Pulse",
    scanner_trigger_code="99",
    convert_to_seconds=["Time"],
    rest_block_codes="crosshair",
    rest_code_pattern="fixed",
    split_cue_from_block=True,
)

events_df = pd.DataFrame(
    {
        "onset": extractor.extract_onsets(),
        "duration": extractor.extract_durations(),
        "trial_type": extractor.extract_trial_types(),
        "mean_rt": extractor.extract_mean_reaction_times(),
    }
)

Creating BIDS Events from E-Prime Logs

from bidsaid.events import EPrimeEventExtractor
import pandas as pd

extractor = EPrimeEventExtractor(
    "sub-01_task-gonogo.txt",
    trial_types="Go|NoGo",  # Can also use ("Go", "NoGo")
    onset_column_name="Stimulus.OnsetTime",
    procedure_column_name="Procedure",
    trigger_column_name="ScannerTrigger.RTTime",
    convert_to_seconds=[
        "Stimulus.OnsetTime",
        "Stimulus.OffsetTime",
        "ScannerTrigger.RTTime",
    ],
)

events_df = pd.DataFrame(
    {
        "onset": extractor.extract_onsets(),
        "duration": extractor.extract_durations(
            offset_column_name="Stimulus.OffsetTime"
        ),
        "trial_type": extractor.extract_trial_types(),
        "reaction_time": extractor.extract_reaction_times(
            reaction_time_column_name="Stimulus.RT"
        ),
    }
)

Audit BIDS Dataset

from bidsaid.audit import BIDSAuditor
from bidsaid.simulate import simulate_bids_dataset

bids_root = simulate_bids_dataset()

auditor = BIDSAuditor(bids_root)
auditor.check_raw_nifti_availability()
auditor.check_raw_sidecar_availability()
auditor.check_events_availability()
auditor.check_preprocessed_nifti_availability()

analysis_dir = bids_root / "first_level"
analysis_sub_dir = analysis_dir / "sub-1" / "ses-1"
analysis_sub_dir.mkdir(parents=True, exist_ok=True)

with open(analysis_sub_dir / "sub-1_task-rest_desc-betas.nii.gz", "w") as f:
    pass

auditor.check_first_level_availability(analysis_dir=analysis_dir, desc="betas")

Compute QC

from bidsaid.qc import create_censor_mask, compute_consecutive_censor_stats

censor_mask = create_censor_mask(
    "confounds.tsv",
    column_name="framewise_displacement",
    threshold=0.5,
    n_dummy_scans=4,
)

consecutive_censor_mean, consecutive_censor_std = compute_consecutive_censor_stats(
    censor_mask, n_dummy_scans=4
)

Surface Movies

import tempfile
from pathlib import Path

import nibabel as nib, numpy as np
from nilearn.image import smooth_img

from bidsaid.movie import (
    MovieWriter,
    compute_vmax,
    create_surface_run,
    mp4_to_gif,
    virtual_display,
)
from bidsaid.simulate import simulate_nifti_image
from bidsaid.surface import fetch_fsaverage_surfaces, get_cortex_masks
from bidsaid.visual import SurfaceRenderer


def simulate_denoised_img():
    nifti_img = simulate_nifti_image((64, 76, 64, 10))
    mask = nifti_img.get_fdata().any(axis=-1)
    data = smooth_img(nifti_img, fwhm=8).get_fdata()
    data[mask] = (data[mask] - data[mask].mean(axis=-1, keepdims=True)) / data[
        mask
    ].std(axis=-1, keepdims=True)
    data[~mask] = 0

    return nib.Nifti1Image(data.astype(np.float32), nifti_img.affine, nifti_img.header)


src_dir = Path(tempfile.mkdtemp())
denoised_files = []
for subject_id, task_name in (
    (subject_id, task_name)
    for subject_id in ("01", "02")
    for task_name in ("rest", "music")
):
    denoised_file = (
        src_dir / f"sub-{subject_id}_task-{task_name}_desc-denoised_bold.nii.gz"
    )
    nib.save(simulate_denoised_img(), denoised_file)
    denoised_files.append(denoised_file)

surfaces = fetch_fsaverage_surfaces("10k")
cortex_masks = get_cortex_masks(surfaces["medial"])

surface_runs = [
    create_surface_run(
        denoised_file,
        surfaces["pial"],
        surfaces["white"],
        cortex_masks,
        n_interpolated_frames=47,
        interpolation_method="cubic",
    )
    for denoised_file in denoised_files
]

threshold = 1.0
vmax = compute_vmax(surface_runs, threshold=threshold)

with (
    virtual_display(),
    SurfaceRenderer(
        *surfaces["inflated"],
        sulcal_depths=surfaces["sulc"],
        color_range=(-vmax, vmax),
        threshold=threshold,
        top_spacing=80,
    ) as renderer,
):
    movie_files = MovieWriter(
        surface_runs,
        renderer,
        task_order=["rest", "music"],
        playback_speed=1,
        label_format="{subject_name}    {task_name}    t = {frame_time:.1f} s",
        task_spacing=40,
    ).write("movies", per_subject=True, per_task=True, shared=True)

gif_file = mp4_to_gif(movie_files[-1], loop=0)

See the API documentation for full parameter details and additional utilities.