NILS - Neuroimaging Intelligent Linked System¶
A comprehensive system for DICOM classification, sorting, anonymization, and BIDS export
Developed at Karolinska Institutet
Department of Clinical Neuroscience, Neuroradiology
What is NILS?¶
NILS (Neuroimaging Intelligent Linked System) is a full-stack application designed for research institutions to efficiently manage neuroimaging data. It provides a complete pipeline from raw DICOM ingestion to BIDS-compliant export.
Core Capabilities¶
Six-Axis Classification System¶
NILS classifies MRI series using six orthogonal axes:
| Axis | Description | Examples |
|---|---|---|
| Base | Contrast weighting | T1w, T2w, PD, DWI, BOLD, SWI |
| Technique | Pulse sequence family | MPRAGE, TSE, FLASH, EPI, GRASE |
| Modifier | Acquisition enhancements | FLAIR, FatSat, MT, IR, PhaseContrast |
| Construct | Derived/map type | ADC, FA, MD, T1Map, T2Map, CBF |
| Provenance | Processing pipeline | SyMRI, SWIRecon, DTIRecon, RawRecon |
| Acceleration | Parallel imaging | GRAPPA, SMS, CAIPIRINHA |
Data Hierarchy¶
NILS organizes imaging data in a 4-level hierarchy:
Subject (Patient)
└── Study (Imaging Session)
└── Series (Acquisition)
└── SeriesStack (Homogeneous Instance Group)
SeriesStack is a key concept - it represents a group of instances within a series that share identical acquisition parameters. This handles multi-echo, multi-flip-angle, and other complex acquisitions.
Documentation¶
- Concepts - Core data models, entities, and terminology
- Cohort Operations - Extraction, Sorting, Anonymization, Export
- Classification - The six-axis detection system
- QC & Viewer - Quality control and image review
Quick Start¶
# Clone and start
git clone https://github.com/NeuroGranberg/NILS.git
cd NILS
./scripts/manage.sh start
# Access web interface
open http://localhost:5173
Requirements¶
- Docker & Docker Compose
- 4GB RAM minimum (8GB recommended)
- Modern web browser
License¶
MIT License - See LICENSE
Citation¶
If you use NILS in your research, please cite:
Chamyani, N. (2025). NILS - Neuroimaging Intelligent Linked System. Karolinska Institutet, Department of Clinical Neuroscience. https://github.com/NeuroGranberg/NILS