Getting Started

Skullduggery removes identifiable facial features from anatomical MRI images while preserving brain tissue, protecting privacy in neuroimaging research.

Install

pip install skullduggery

Your First Command

skullduggery /path/to/bids/dataset --participant-label 01 --report-dir ./test_reports

Common Commands

Goal	Command
Process everyone	`skullduggery /path/to/dataset`
Specific participants	`skullduggery /path/to/dataset --participant-label 01 02 03`
Specific sessions	`skullduggery /path/to/dataset --session-label 01`
With reports	`skullduggery /path/to/dataset --report-dir ./reports`
Pediatric data	`skullduggery /path/to/dataset --template MNIInfant:cohort-06m09m`
All options	`skullduggery --help`

Next Steps

Usage Guide - All command-line options
Command Reference - Quick lookup
Examples - Real-world scenarios