VoxelOps Documentation

Clean, simple neuroimaging pipeline automation for brain banks.

Brain banks need to process neuroimaging data consistently, reproducibly, and auditably. VoxelOps makes that simple by wrapping Docker-based neuroimaging tools into clean Python functions that return plain dicts – ready for your database, your logs, and your peace of mind.

Overview

docs
tests, CI & coverage
version
styling
license

Features

Simple Functions – No classes, no inheritance – just run_*() functions that return dicts
Clear Schemas – Typed dataclass inputs, outputs, and defaults for every procedure
Reproducibility – The exact Docker command is stored in every execution record
Database-Ready – Results are plain dicts, trivial to save to PostgreSQL, MongoDB, or JSON
Brain Bank Defaults – Define your standard parameters once, reuse across all participants
Comprehensive Logging – Every run logged to JSON with timestamps, duration, and exit codes

Available Procedures

Procedure	Purpose	Function	Execution
HeudiConv	DICOM to BIDS conversion	`run_heudiconv()`	Docker
QSIPrep	Diffusion MRI preprocessing	`run_qsiprep()`	Docker
QSIRecon	Diffusion reconstruction & connectivity	`run_qsirecon()`	Docker
QSIParc	Parcellation via `parcellate`	`run_qsiparc()`	Python (direct)

Installation

pip install voxelops

Requirements: Python >= 3.8, Docker installed and accessible.