VoxelOps Documentation

Documentation Status

Clean, simple neuroimaging pipeline automation for brain banks.

VoxelOps wraps Docker-based neuroimaging tools into clean Python functions that return plain dicts – ready for your database, your logs, and your peace of mind.

from voxelops import run_qsiprep, QSIPrepInputs

result = run_qsiprep(
    QSIPrepInputs(bids_dir="/data/bids", participant="01"),
    nprocs=16,
)

print(result["duration_human"])   # "1:30:00"
print(result["command"])          # exact Docker command for reproducibility

Key Features

Simple functions – run_*() functions that return dicts, no classes or inheritance
Typed schemas – 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 persist anywhere
Brain bank defaults – define standard parameters once, reuse everywhere

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.

Contents

Indices and tables