parcellate 0.3.0

A simple tool for extracting regional statistics from scalar neuroimaging maps.

parcellate

Extract regional statistics from scalar neuroimaging maps using atlas-based parcellation.

What It Does

parcellate is a Python tool that extracts regional statistics from volumetric brain images using atlas-based parcellation. Given a scalar map (e.g., gray matter density, fractional anisotropy) and a labeled atlas, it computes summary statistics for each brain region.

Key Features:

• 🧠 Multiple Pipeline Support: Integrates with CAT12 (VBM) and QSIRecon (diffusion MRI) outputs
• 📊 Rich Statistics: 45 built-in metrics in three tiers (core / extended / diagnostic), including robust statistics, higher-order moments, and normality tests
• ⚡ Performance: Parallel processing, smart caching, and optimized resampling
• 📁 BIDS App: Follows BIDS App positional-argument conventions
• 🔧 Flexible: Python API and CLI interfaces, custom atlases and statistics

Supported Input Formats:

• CAT12: Gray matter (GM), white matter (WM), CSF volumes, cortical thickness maps
• QSIRecon: Diffusion scalar maps (FA, MD, AD, RD, etc.)

Output Format:

• TSV files with regional statistics (one row per brain region)
• BIDS-derivative compatible directory structure

Installation

pip install parcellate

For CAT12 CSV batch processing with environment variable support:

pip install parcellate[dotenv]

Quick Start

BIDS App interface (recommended)

parcellate follows the BIDS App convention:

parcellate <bids_dir> <output_dir> participant --pipeline {cat12,qsirecon} --config config.toml

Create a minimal TOML file with your atlas definitions:

# config.toml
[[atlases]]
name  = "schaefer400"
path  = "/atlases/Schaefer2018_400Parcels_7Networks_order_FSLMNI152_1mm.nii.gz"
lut   = "/atlases/Schaefer2018_400Parcels_7Networks_order_FSLMNI152.tsv"
space = "MNI152NLin2009cAsym"

CAT12

parcellate /data/cat12_derivatives /data/parcellations participant \
    --pipeline cat12 \
    --config config.toml \
    --stat-tier extended

QSIRecon

parcellate /data/qsirecon_derivatives /data/parcellations participant \
    --pipeline qsirecon \
    --config config.toml \
    --stat-tier core \
    --n-procs 4

Common options

Flag	Description
--participant-label 01 02	Process only these subjects
--session-label ses-01	Process only this session
--mask gm / --mask /path/to/mask.nii.gz	Brain mask (CAT12 default: gm)
--mask-threshold 0.5	Minimum mask probability
--stat-tier core|extended|diagnostic	Statistics tier (default: diagnostic)
--force	Overwrite existing outputs
--n-jobs N	Within-subject parallelism
--n-procs N	Across-subject parallelism

See the CLI reference for the full list of flags.

Legacy interface (deprecated)

The old subcommand syntax still works but emits a DeprecationWarning:

# Deprecated — use BIDS App interface above
parcellate cat12 config.toml
parcellate qsirecon config.toml

Configuration Reference

TOML Configuration

Field	Type	Description	Default
input_root	string	Path to preprocessing derivatives	Required
output_dir	string	Output directory for parcellations	Required
subjects	list	Subject IDs to process	All discovered
sessions	list	Session IDs to process	All discovered
mask	string	Brain mask path or builtin (gm, wm, brain)	gm (CAT12) / none (QSIRecon)
mask_threshold	float	Minimum mask value to include a voxel	0.0
stat_tier	string	Statistics tier (core, extended, diagnostic, all)	diagnostic
force	boolean	Overwrite existing outputs	false
log_level	string	Logging verbosity (DEBUG, INFO, WARNING, ERROR)	INFO
n_jobs	integer	Parallel jobs within subject	1
n_procs	integer	Parallel processes across subjects	1

Atlas Definition

[[atlases]]
name            = "MyAtlas"                   # Atlas identifier
path            = "/path/to/atlas.nii.gz"     # NIfTI file (3D integer or 4D probabilistic)
lut             = "/path/to/atlas.tsv"        # Optional: TSV with 'index' and 'label' columns
space           = "MNI152NLin2009cAsym"       # Template space
atlas_threshold = 0.0                         # For 4D atlases: minimum voxel probability

For the full configuration reference, see the Configuration reference.

Output Format

Each parcellation produces a TSV file with one row per brain region and one column per statistic. The first two columns are always:

Column	Description
index	Integer region index from the atlas
label	Region name from the lookup table

Subsequent columns contain the computed statistics. Which columns appear depends on the selected stat_tier. For CAT12, a vol_TIV column is also appended when XML report files are found.

A JSON sidecar (.json) is written alongside each TSV with full provenance (atlas path, mask, thresholds, software version, timestamp).

Statistics tiers

parcellate ships with 45 built-in statistics organized into tiers. Select a tier with --stat-tier (CLI) or stat_tier (TOML / Python):

Tier	Count	Typical use
core	6	Fast exploration, large cohorts
extended	21	Production pipelines
diagnostic (default)	45	QC, distribution inspection

Core statistics: mean, std, median, volume_mm3, voxel_count, sum

Extended adds: robust means (MAD, z-score, IQR filtered), dispersion (cv, robust_cv), shape (skewness, excess_kurtosis), key percentiles (5th, 25th, 75th, 95th)

Diagnostic adds: normality tests (Shapiro-Wilk, D'Agostino K²), outlier proportions, tail mass, entropy, boolean QC flags

See the full Metrics reference for descriptions of all 45 statistics.

Python API

Use the core parcellation engine directly:

from parcellate import VolumetricParcellator
import nibabel as nib

# Initialize parcellator
parcellator = VolumetricParcellator(
    atlas_img="atlas.nii.gz",
    lut="atlas.tsv",
    mask="gm",                  # built-in MNI152 grey-matter mask
    stat_tier="extended",       # 21 statistics (default: all 45)
    resampling_target="data",   # resample atlas to scalar-map space
)

# Fit once, then transform one or more maps
parcellator.fit("gm_map.nii.gz")
stats = parcellator.transform("gm_map.nii.gz")
print(stats.head())

Custom statistics

Supply a dict of callables to override the built-in statistics entirely:

import numpy as np

parcellator = VolumetricParcellator(
    atlas_img="atlas.nii.gz",
    stat_functions={
        "iqr": lambda x: float(np.nanpercentile(x, 75) - np.nanpercentile(x, 25)),
        "q90": lambda x: float(np.nanpercentile(x, 90)),
    },
)

Development

Setup

# Clone repository
git clone https://github.com/GalKepler/parcellate.git
cd parcellate

# Install development dependencies
make install

# Run tests
make test

# Run code quality checks
make check

Running Tests

# All tests
uv run python -m pytest

# Specific test file
uv run python -m pytest tests/test_parcellator.py

# With coverage
uv run python -m pytest --cov=src/parcellate --cov-report=html

Contributing

1. Fork the repository
2. Create a feature branch (git checkout -b feature/amazing-feature)
3. Make your changes
4. Run tests and quality checks (make check && make test)
5. Commit your changes (git commit -m 'Add amazing feature')
6. Push to the branch (git push origin feature/amazing-feature)
7. Open a Pull Request

Documentation

Full documentation is available at https://GalKepler.github.io/parcellate/

License

This project is licensed under the MIT License - see the LICENSE file for details.

Citation

If you use this tool in your research, please cite:

@software{parcellate,
  author = {Kepler, Gal},
  title = {parcellate: Atlas-based parcellation of neuroimaging data},
  url = {https://github.com/GalKepler/parcellate},
  year = {2024}
}

Acknowledgments

Repository initiated with fpgmaas/cookiecutter-uv.