BCBlib

A collection of neuroimaging utilities for MRI data analysis, developed by Chris Foulon at the BCBlab. The library covers NIfTI image processing, FSL workflow integration, and research-grade statistical tools — several of which have been used in published studies on structural connectivity, lesion-symptom mapping, and stroke outcome prediction.

pip install bcblib

Quick Start

# Load and inspect a NIfTI image
from bcblib.imaging import load_nifti, image_stats
nii = load_nifti("subject01_lesion.nii.gz")
stats = image_stats(nii)

# Balanced dataset splitting for cross-validation
from bcblib.tools.dataset_splitting import permutation_balanced_splits
folds, score, report = permutation_balanced_splits(
    groups=has_chronic,
    covariates={"acute_vol": acute_volumes, "chronic_vol": chronic_volumes},
    n_splits=5,
    n_permutations=50000,
    seed=42,
)

# Prepare FSL randomise inputs from a spreadsheet
from bcblib.tools.randomise_helper import spreadsheet_to_mat_and_file_list
spreadsheet_to_mat_and_file_list(
    "subjects.csv", columns=["age", "score"],
    output_dir="randomise_inputs/", filenames_column="image_path"
)

Modules

Imaging (bcblib.imaging)

A modern FSL-equivalent API for NIfTI image processing. All functions accept either a file path or an already-loaded Nifti1Image.

Module	Description
bcblib.imaging.io	Load, save, resave NIfTI images; format detection
bcblib.imaging.info	Header inspection — equivalent to fslinfo
bcblib.imaging.stats	Centre of gravity, volume, histogram, laterality
bcblib.imaging.math	Binarize, dilate, erode, apply/invert masks
bcblib.imaging.orient	Get and reorient image orientation
bcblib.imaging.manipulate	Extract ROI, merge, split 4-D images
bcblib.imaging.convert	Convert between .nii and .nii.gz

Backward compatibility: bcblib.tools.nifti_utils, bcblib.tools.images_utils, and bcblib.tools.nii_stats are kept as shims. New code should import from bcblib.imaging directly.

Research Tools (bcblib.tools)

lesion_features — End-to-end pipeline for extracting atlas-based overlap profiles from patient lesion masks and disconnectome maps. See docs/lesion_features_pipeline.md for full usage.

damage_profile Compute overlap statistics between a subject map (lesion or disconnectome) and one or more brain atlases. Returns a DataFrame per atlas with per-region voxel counts, coverage fraction, mean overlap, and percentiles.

best_overlap Compute preserved structural connectivity from patient and cluster disconnectome maps using Bayesian modelling (PyMC). Outputs latent connectivity scores with uncertainty estimates per brain region.

dataset_splitting Monte Carlo permutation search for the most balanced k-way dataset split. Balances group counts (round-robin hard constraint) and continuous covariate distributions (Kruskal-Wallis minimax score). Returns fold indices, best score, and a full JSON report including convergence history and per-fold descriptive stats. See Publications.

randomise_helper Build FSL randomise inputs from a spreadsheet: generates .mat design files, concatenates 4-D NIfTI stacks, and manages file lists. See Publications.

split_clusters — Split a multi-label NIfTI atlas into one file per label value.

divide_mask — Cluster a binary mask into spatially separate components by proximity.

shapes — Generate geometric shapes (hyperspheres, arbitrary forms) as NIfTI arrays, useful for creating synthetic phantom data.

constants — Pre-computed MNI 1 mm and 2 mm affines and shapes; empty_MNI1MM() / empty_MNI2MM() convenience constructors.

general_utils — JSON I/O with support for NumPy arrays, UUIDs, and datetime objects.

spreadsheet_io_utils — Load CSV and Excel files with column selection helpers.

dataframe_filtering — Remove constant columns, filter by completeness threshold, handle datetime columns for ML pipelines.

mat_transform — Connectivity matrix preprocessing: log₂ transform, z-score normalisation, rank transform.

arrays_utils — Coordinate validation and centroid calculations for NumPy arrays.

umap_utils — UMAP dimensionality reduction wrappers tuned for neuroimaging data.

visualisation — Wrappers for MRIcron, matplotlib, and TensorBoard visualisation.

Requires external tools (MRIcron, TensorBoard) installed separately depending on which functions are used.

CLI Tools

Command	Example	Description
bcb-info	bcb-info brain.nii.gz	NIfTI header summary (fslinfo equivalent)
bcb-header	bcb-header brain.nii.gz	Full NIfTI header inspection
bcb-stats	bcb-stats lesion.nii.gz	Image statistics (fslstats equivalent)
bcb-orient	bcb-orient -g brain.nii.gz	Get or set image orientation
bcb-roi	bcb-roi brain.nii.gz mask.nii.gz	Extract a region of interest
bcb-merge	bcb-merge -o 4d.nii.gz *.nii.gz	Merge NIfTI images along a dimension
bcb-split	bcb-split 4d.nii.gz -o out/	Split a 4-D NIfTI along the volume axis
bcb-convert	bcb-convert brain.nii	Convert between .nii and .nii.gz
bcb-dataset-split	see below	Balanced dataset splitting from a CSV file
bcb-lf-preprocess	see below	Stage 1: normalise lesions to MNI6 1mm + compute disconnectomes
bcb-lesion-features	see below	Stage 2: extract atlas overlap features from prep output
bcb-damage-profile	see below	Overlap statistics between a subject map and brain atlases
randomise_helper	—	Build FSL randomise design files from a spreadsheet
pick_up_matched_synth_lesions	—	Select synthetic lesions matching a size distribution

# Stage 1: normalise lesions to MNI152NLin6Asym 1mm and compute disconnectomes
bcb-lf-preprocess \
    --bids-dir /data/stroke_cohort \
    --output-dir /data/stroke_cohort_prep \
    --bcbtoolkit /opt/BCBToolKit \
    --tracks-dir /opt/BCBToolKit/Tools/extraFiles/tracks_1mm \
    --ncores 8 \
    --tmpdir /scratch/disco_tmp   # set on JupyterHub/HPC if /tmp is restricted

# Stage 2: extract atlas overlap features (downloads atlases on first run)
bcb-lesion-features \
    --prep-dir /data/stroke_cohort_prep \
    --output-dir /data/stroke_cohort_features \
    --ebrains --assume-yes

# Balanced dataset split — writes splits.csv and splits_report.json
bcb-dataset-split \
    --input subjects.csv \
    --group-col has_chronic \
    --covariate-cols acute_volume chronic_volume \
    --n-splits 5 --n-permutations 50000 --seed 42 \
    --output splits.csv

# Damage profile — overlap between a lesion map and the Rojkova WM atlas
bcb-damage-profile \
    --map lesion.nii.gz \
    --preset rojkova \
    --output-dir ./results

# Custom atlas directory, explicit threshold
bcb-damage-profile \
    --map disconnectome.nii.gz \
    --atlas /path/to/atlas_dir --name my_atlas --threshold 0.2 \
    --output-dir ./results

Dependencies

Core dependencies installed automatically:

• nibabel, numpy, scipy, nilearn, scikit-learn
• pandas, openpyxl
• tqdm, joblib, statsmodels
• matplotlib, rich
• pymc >= 5, arviz (required for best_overlap)
• umap-learn (required for umap_utils)
• mne
• templateflow, nitransforms (required for damage_profile cross-template resampling)

External tools (not installed by pip):

• FSL — required for randomise_helper to call randomise itself
• MRIcron — required for visualisation MRIcron wrappers
• TensorBoard — required for visualisation TensorBoard integration

Publications

Tools from BCBlib have been used in the following publications:

• randomise_helper — Giampiccolo D, Binding LP, Caciagli L, Rodionov R, Foulon C, et al. (2023). Thalamostriatal disconnection underpins long-term seizure freedom in frontal lobe epilepsy surgery. Brain, 146(6):2377–2388. https://doi.org/10.1093/brain/awad085

• pick_up_matched_synth_lesions — Thiebaut de Schotten M, Foulon C, Nachev P. (2020). Brain disconnections link structural connectivity with function and behaviour. Nature Communications, 11:5094. https://doi.org/10.1038/s41467-020-18920-9

• dataset_splitting — Foulon C, Gray R, Ruffle JK, et al. (2025). Generalizable automated ischaemic stroke lesion segmentation with vision transformers. arXiv:2502.06939. https://arxiv.org/abs/2502.06939

• BCBlib was used to participate in the Neural-CUP benchmark — Matsulevits A, Alvez P, Atzori M, et al. (2024). A global effort to benchmark predictive models and reveal mechanistic diversity in long-term stroke outcomes. bioRxiv. https://doi.org/10.1101/2024.10.17.618691

• BCBlib is used in — Foulon C, Ovando-Tellez M, Talozzi L, Corbetta M, Matsulevits A, Thiebaut de Schotten M. (2024). Emerging-properties Mapping Using Spatial Embedding Statistics: EMUSES. arXiv:2406.14309 (preprint). https://arxiv.org/abs/2406.14309

Links

• Source
• Bug reports
• BCBlab
• PyPI