Olga Ciccarelli

33 papers A 1Journal 28Unranked 4
YearRankTypeTitle / Venue / Authors
2023 J jnl
Pattern Recognit.
Le Zhang, Ryutaro Tanno, Moucheng Xu, Yawen Huang, Kevin Bronik, Chen Jin, Joseph Jacob, Yefeng Zheng, Ling Shao, Olga Ciccarelli, Frederik Barkhof, Daniel C. Alexander
2023 J jnl
Frontiers Neuroinformatics
Antonio Ricciardi, Francesco Grussu, Baris Kanber, Ferran Prados, Marios C. Yiannakas, Bhavana S. Solanky, Frank Riemer, Xavier Golay, Wallace Brownlee, Olga Ciccarelli, Daniel C. Alexander, Claudia A. M. Gandini Wheeler-Kingshott
2021 J jnl
NeuroImage
Ioana Hill, Marco Palombo, Mathieu D. Santin, Francesca Branzoli, Anne-Charlotte Philippe, Demian Wassermann, Marie-Stephane Aigrot, Bruno Stankoff, Anne Baron-Van Evercooren, Mehdi Felfli, Dominique Langui, Hui Zhang, Stéphane Lehéricy, Alexandra Petiet, Daniel C. Alexander, Olga Ciccarelli, Ivana Drobnjak
2020 J jnl
CoRR
Le Zhang, Ryutaro Tanno, Mou-Cheng Xu, Chen Jin, Joseph Jacob, Olga Ciccarelli, Frederik Barkhof, Daniel C. Alexander
2020 J jnl
NeuroImage
Ferran Prados, Marcello Moccia, Aubrey Johnson, Marios C. Yiannakas, Francesco Grussu, Manuel Jorge Cardoso, Olga Ciccarelli, Sébastien Ourselin, Frederik Barkhof, Claudia A. M. Wheeler-Kingshott
2020 conf
MICCAI (1)
Le Zhang, Ryutaro Tanno, Kevin Bronik, Chen Jin, Parashkev Nachev, Frederik Barkhof, Olga Ciccarelli, Daniel C. Alexander
2020 J jnl
Neuroinformatics
Baris Kanber, James K. Ruffle, M. Jorge Cardoso, Sébastien Ourselin, Olga Ciccarelli
2019 J jnl
npj Digit. Medicine
Baris Kanber, Parashkev Nachev, Frederik Barkhof, Alberto Calvi, Jorge Cardoso, Rosa Cortese, Ferran Prados, Carole H. Sudre, Carmen Tur, Sébastien Ourselin, Olga Ciccarelli
2019 J jnl
npj Digit. Medicine
Baris Kanber, Parashkev Nachev, Frederik Barkhof, Alberto Calvi, Jorge Cardoso, Rosa Cortese, Ferran Prados, Carole H. Sudre, Carmen Tur, Sébastien Ourselin, Olga Ciccarelli
2018 J jnl
CoRR
Charley Gros, Benjamin De Leener, Atef Badji, Josefina Maranzano, Dominique Eden, Sara M. Dupont, Jason Talbott, Ren Zhuoquiong, Yaou Liu, Tobias Granberg, Russell Ouellette, Yasuhiko Tachibana, Masaaki Hori, Kouhei Kamiya, Lydia Chougar, Leszek Stawiarz, Jan Hillert, Elise Bannier, Anne Kerbrat, Gilles Edan, Pierre Labauge, Virginie Callot, Jean Pelletier, Bertrand Audoin, Henitsoa Rasoanandrianina, Jean-Christophe Brisset, Paola Valsasina, Maria Assunta Rocca, Massimo Filippi, Rohit Bakshi, Shahamat Tauhid, Ferran Prados, Marios C. Yiannakas, Hugh Kearney, Olga Ciccarelli, Seth A. Smith, Constantina Andrada Treaba, Caterina Mainero, Jennifer Lefeuvre, Daniel S. Reich, Govind Nair, Vincent Auclair, Donald G. McLaren, Allan R. Martin, Michael G. Fehlings, Shahabeddin Vahdat, Ali Khatibi, Julien Doyon, Timothy M. Shepherd, Erik Charlson, Sridar Narayanan, Julien Cohen-Adad
2017 J jnl
NeuroImage
Aaron Carass, Snehashis Roy, Amod Jog, Jennifer L. Cuzzocreo, Elizabeth M. Sweeney, Adrian Gherman, Julia Button, James Nguyen, Ferran Prados, Carole H. Sudre, Manuel Jorge Cardoso, Niamh Cawley, Olga Ciccarelli, Claudia A. M. Wheeler-Kingshott, Sébastien Ourselin, Laurence Catanese, Hrishikesh Deshpande, Pierre Maurel, Olivier Commowick, Christian Barillot, Xavier Tomas-Fernandez
2017 J jnl
NeuroImage
Gemma L. Nedjati-Gilani, Torben Schneider, Matt G. Hall, Niamh Cawley, Ioana Hill, Olga Ciccarelli, Ivana Drobnjak, Claudia A. M. Gandini Wheeler-Kingshott, Daniel C. Alexander
2017 J jnl
NeuroImage
Alexandra de Sitter, Martijn D. Steenwijk, Aurélie Ruet, Adriaan Versteeg, Yaou Liu, Ronald A. van Schijndel, Petra J. W. Pouwels, Iris D. Kilsdonk, Keith S. Cover, Bob W. van Dijk, Stefan Ropele, Maria Assunta Rocca, Marios C. Yiannakas, Mike P. Wattjes, Soheil Damangir, Giovanni B. Frisoni, Jaume Sastre-Garriga, Alex Rovira, Christian Enzinger, Massimo Filippi, Jette L. Frederiksen, Olga Ciccarelli, Ludwig Kappos, Frederik Barkhof, Hugo Vrenken
2016 J jnl
NeuroImage
Ferran Prados, Manuel Jorge Cardoso, Baris Kanber, Olga Ciccarelli, Raju Kapoor, Claudia A. M. Wheeler-Kingshott, Sébastien Ourselin
2016 conf
BrainLes@MICCAI
Ferran Prados, M. Jorge Cardoso, Niamh Cawley, Baris Kanber, Olga Ciccarelli, Claudia A. M. Wheeler-Kingshott, Sébastien Ourselin
2014 J jnl
NeuroImage
Arman Eshaghi, Benedetta Bodini, Gerard R. Ridgway, Daniel García-Lorenzo, Daniel J. Tozer, Mohammad Ali Sahraian, Alan J. Thompson, Olga Ciccarelli
2014 J jnl
NeuroImage
Claudia A. M. Wheeler-Kingshott, Patrick W. Stroman, J. M. Schwab, M. Bacon, Rachael L. Bosma, Jonathan C. W. Brooks, D. W. Cadotte, T. Carlstedt, Olga Ciccarelli, Julien Cohen-Adad, Armin Curt, Nikos Evangelou, Michael G. Fehlings, Massimo Filippi, B. J. Kelley, Spyros S. Kollias, Alex L. MacKay, Carlo A. Porro, Seth A. Smith, S. M. Strittmatter, Paul E. Summers, Alan J. Thompson, Irene Tracey
2014 J jnl
NeuroImage
Patrick W. Stroman, Claudia A. M. Wheeler-Kingshott, M. Bacon, J. M. Schwab, Rachael L. Bosma, Jonathan C. W. Brooks, D. W. Cadotte, T. Carlstedt, Olga Ciccarelli, Julien Cohen-Adad, Armin Curt, Nikos Evangelou, Michael G. Fehlings, Massimo Filippi, B. J. Kelley, Spyros S. Kollias, Alex L. MacKay, Carlo A. Porro, Seth A. Smith, S. M. Strittmatter, Paul E. Summers, Irene Tracey
2013 conf
PRNI
Viktor Wottschel, Olga Ciccarelli, Declan T. Chard, David H. Miller, Daniel C. Alexander
2012 J jnl
NeuroImage
Marios C. Yiannakas, Hugh Kearney, R. S. Samson, Declan T. Chard, Olga Ciccarelli, David H. Miller, Claudia A. M. Wheeler-Kingshott
2012 J jnl
NeuroImage
Daniel J. Tozer, Declan T. Chard, Benedetta Bodini, Olga Ciccarelli, David H. Miller, Alan J. Thompson, Claudia A. M. Wheeler-Kingshott
2011 conf
MLINI
Philip P. Kwok, Olga Ciccarelli, Declan T. Chard, David H. Miller, Daniel C. Alexander
2009 J jnl
NeuroImage
Laura Mancini, Olga Ciccarelli, F. Manfredonia, John S. Thornton, Federica Agosta, Frederik Barkhof, Christian F. Beckmann, Nicola De Stefano, Christian Enzinger, Franz Fazekas, Massimo Filippi, Achim Gass, Jochen G. Hirsch, Heidi Johansen-Berg, Ludwig Kappos, T. Korteweg, S. C. Manson, Silvia Marino, Paul M. Matthews, Xavier Montalban, Jackie Palace, Chris Polman, Maria Assunta Rocca, Stefan Ropele, Alex Rovira, C. Wegner, Karl J. Friston, Alan J. Thompson, Tarek A. Yousry
2008 J jnl
NeuroImage
Rose Bosnell, C. Wegner, Zsigmond Tamás Kincses, T. Korteweg, Federica Agosta, Olga Ciccarelli, Nicola De Stefano, Achim Gass, Jochen G. Hirsch, Heidi Johansen-Berg, Ludwig Kappos, Frederik Barkhof, Laura Mancini, F. Manfredonia, Silvia Marino, David H. Miller, Xavier Montalban, Jackie Palace, Maria Assunta Rocca, Christian Enzinger, Stefan Ropele, Alex Rovira, Stephen M. Smith, Alan J. Thompson, John S. Thornton, Tarek A. Yousry, Brandon J. Whitcher, Massimo Filippi, Paul M. Matthews
2007 J jnl
NeuroImage
Z. Khaleeli, Mara Cercignani, Bertrand Audoin, Olga Ciccarelli, David H. Miller, Alan J. Thompson
2006 J jnl
NeuroImage
Stephen M. Smith, Mark Jenkinson, Heidi Johansen-Berg, Daniel Rueckert, Thomas E. Nichols, Clare E. Mackay, Kate E. Watkins, Olga Ciccarelli, M. Zaheer Cader, Paul M. Matthews, Timothy Edward John Behrens
2005 A conf
MICCAI
Philip A. Cook, Hui Zhang, Brian B. Avants, Paul A. Yushkevich, Daniel C. Alexander, James C. Gee, Olga Ciccarelli, Alan J. Thompson
2005 J jnl
NeuroImage
Geoffrey J. M. Parker, Simona Luzzi, Daniel C. Alexander, Claudia A. M. Wheeler-Kingshott, Olga Ciccarelli, Matthew A. Lambon Ralph
2004 J jnl
NeuroImage
Ahmed T. Toosy, Olga Ciccarelli, Geoff J. M. Parker, Claudia A. M. Wheeler-Kingshott, David H. Miller, Alan J. Thompson
2003 J jnl
NeuroImage
Olga Ciccarelli, Ahmed T. Toosy, Geoffrey J. M. Parker, Claudia A. M. Gandini Wheeler-Kingshott, Gareth J. Barker, David H. Miller, Alan J. Thompson
2003 J jnl
NeuroImage
Olga Ciccarelli, Geoffrey J. M. Parker, Ahmed T. Toosy, Claudia A. M. Gandini Wheeler-Kingshott, Gareth J. Barker, Philip A. Boulby, David H. Miller, Alan J. Thompson
2002 J jnl
NeuroImage
Geoffrey J. M. Parker, Klaas E. Stephan, Gareth J. Barker, James B. Rowe, David G. MacManus, Claudia A. M. Wheeler-Kingshott, Olga Ciccarelli, Richard E. Passingham, Rachel L. Spinks, Roger N. Lemon, Robert Turner
2002 J jnl
NeuroImage
Claudia A. M. Wheeler-Kingshott, Simon J. Hickman, Geoffrey J. M. Parker, Olga Ciccarelli, Mark R. Symms, David H. Miller, Gareth J. Barker
Docker-README.md
← Index Docker-README.md markdown
# REDB Docker Setup

This document describes the Docker containerization for the REDB malware analysis framework.

## Overview

REDB has been containerized as a single unified image that supports both feature extraction and decompilation analysis. The container is stateless, processes files from S3 or local mounts, and exports results to ClickHouse database or via API callbacks.

## Architecture

- **Single Unified Container**: One image handles both feature extraction and decompilation
- **Runtime Tool Installation**: Tools (CAPA, DIE, Binary Ninja) installed at runtime from host snapshots
- **Stateless Processing**: No persistent storage required between runs
- **Multiple Invocation Modes**: Supports `--nomad-job`, `--s3`, `--s3-solo`, and `--path` modes
- **External Dependencies**: Connects to external ClickHouse and S3 services

## Files Structure

```
├── Dockerfile                 # Single unified container definition
├── docker-build.sh            # Build script with Docker Desktop bug workaround
├── docker-push.sh             # Push script to registry
├── test-docker.sh             # Container testing script
├── test-nomad.sh              # Nomad job mode testing
├── .dockerignore              # Build context exclusions
└── scripts/
    └── setup-and-run.sh       # Runtime tool setup entrypoint
```

## Tool Installation Strategy

The container uses a **runtime installation** approach:

1. **Base Image**: Contains Python dependencies and REDB code
2. **Runtime Setup**: `scripts/setup-and-run.sh` configures tools at container start
3. **Host Snapshots**: Binary Ninja installed from `/opt/binaryninja` if available
4. **System Tools**: CAPA and DIE expected at `/usr/bin/capa` and `/usr/bin/nfdc`

## Build and Run

### 1. Build Container

```bash
# Build unified image
./docker-build.sh

# Manual build
docker build --platform linux/amd64 -f Dockerfile -t redb:latest .
```

### 2. Run Modes

#### Nomad Job Mode (Primary)
```bash
# Feature extraction
docker run --rm \
  -e JOB_ID="analysis_001" \
  -e S3_KEY="samples/malware.exe" \
  -e S3_BUCKET="malware-bucket" \
  -e WORKER_TYPE="feature_extraction" \
  -e CALLBACK_URL="https://api.example.com/callbacks" \
  -e ANALYSIS_MODULES="BasicPropertiesExtractor,PEFeaturesExtractor" \
  -e CLICKHOUSE_HOST="clickhouse.example.com" \
  -e S3_ENDPOINT="s3.example.com" \
  -e S3_ACCESS_KEY="your-key" \
  -e S3_SECRET_KEY="your-secret" \
  redb:latest python3 start.py --nomad-job

# Decompilation (same container, different flags)
docker run --rm \
  -e JOB_ID="analysis_002" \
  -e S3_KEY="samples/malware.exe" \
  -e S3_BUCKET="malware-bucket" \
  -e WORKER_TYPE="decompilation" \
  -e CALLBACK_URL="https://api.example.com/callbacks" \
  -e ANALYSIS_MODULES="all" \
  -v /opt/binaryninja:/opt/binaryninja:ro \
  redb:latest python3 start.py --nomad-job --decompile
```

#### S3 Solo Mode
```bash
# Process single sample by S3 key (standard sharded path)
docker run --rm \
  -e S3_BUCKET="samples-bucket" \
  -e CLICKHOUSE_HOST="clickhouse.example.com" \
  -e S3_ENDPOINT="s3.example.com" \
  -e INDEX_PREFIX="redb" \
  -e REPO="test-analysis" \
  redb:latest python3 start.py --s3-solo "09/f7/09f7d02a3c2382199458c98a62b045145ee54ab6aba86166aecf3d10c3c1444c.zip"

# Process private sample (with prepath)
docker run --rm \
  -e S3_BUCKET="samples-bucket" \
  -e CLICKHOUSE_HOST="clickhouse.example.com" \
  -e S3_ENDPOINT="s3.example.com" \
  -e INDEX_PREFIX="redb" \
  -e REPO="test-analysis" \
  redb:latest python3 start.py --s3-solo "private/ab/cd/abcd1234567890abcdef1234567890abcdef1234567890abcdef123456.zip"
```

#### Local Files Mode
```bash
# Mount local samples
docker run --rm \
  -v /path/to/samples:/samples:ro \
  -v ./logs:/app/logs \
  -e CLICKHOUSE_HOST="clickhouse.example.com" \
  redb:latest python3 start.py --path /samples --repo local_test --index_prefix redb
```

## Environment Variables

### Required for Nomad Job Mode
- `JOB_ID` - Unique job identifier
- `S3_KEY` - S3 object key for sample
- `S3_BUCKET` - S3 bucket name
- `WORKER_TYPE` - "feature_extraction" or "decompilation"
- `CALLBACK_URL` - API endpoint for results
- `ANALYSIS_MODULES` - Comma-separated extractor list or "all"

### Database Configuration
- `CLICKHOUSE_HOST` - ClickHouse server hostname
- `CLICKHOUSE_PORT` - Port (default: 8123)
- `CLICKHOUSE_USER` - Database user (default: default)
- `CLICKHOUSE_PASSWORD` - Database password
- `CLICKHOUSE_DATABASE` - Database name (default: default)

### S3 Configuration
- `S3_ENDPOINT` - S3 endpoint URL
- `S3_ACCESS_KEY` - S3 access key
- `S3_SECRET_KEY` - S3 secret key
- `S3_SECURE` - "true" or "false" for HTTPS

### Processing Configuration
- `INDEX_PREFIX` - Database table prefix (default: redb)
- `REPO` - Repository identifier for this analysis batch
- `BATCH_SIZE` - Processing batch size (default: 10)
- `REDB_TIMEOUT` - Analysis timeout in seconds (default: 300)

### Tool Timeouts
- `CAPA_TIMEOUT` - CAPA analysis timeout (default: 300)
- `DIE_TIMEOUT` - DIE analysis timeout (default: 180)
- `BINJA_TIMEOUT` - Binary Ninja timeout (default: 1200)
- `DECOMPILE_EXTRACTOR_TIMEOUT` - Decompilation timeout (default: 2580)

## Binary Ninja Setup

For decompilation capabilities, mount Binary Ninja from host:

```bash
# Mount Binary Ninja installation
-v /opt/binaryninja:/opt/binaryninja:ro

# Mount license file
-v /path/to/license.dat:/home/analyzer/.binaryninja/license.dat:ro
```

The container will automatically detect and configure Binary Ninja at runtime.

## Registry Deployment

### Push to Registry
```bash
# Tag and push
./docker-push.sh

# Or manually
docker tag redb:latest your-registry/redb:latest
docker push your-registry/redb:latest
```

### Pull and Run
```bash
docker pull your-registry/redb:latest
docker run your-registry/redb:latest python3 start.py --nomad-job
```

## Testing

### Container Functionality Test
```bash
# Test with S3 key (standard sharded path)
./test-docker.sh "09/f7/09f7d02a3c2382199458c98a62b045145ee54ab6aba86166aecf3d10c3c1444c.zip"

# Test with private sample S3 key
./test-docker.sh "private/ab/cd/abcd1234567890abcdef1234567890abcdef1234567890abcdef123456.zip"
```

### Nomad Job Architecture Test
```bash
# Test Nomad job mode
./test-nomad.sh
```

## Development

### Interactive Container
```bash
# Debug container interactively
docker run -it --entrypoint /bin/bash redb:latest

# Check tool availability
docker run --rm redb:latest which python3
docker run --rm redb:latest ls -la /usr/bin/capa
```

### Build Troubleshooting

The build script includes workarounds for Docker Desktop bugs:

```bash
# If build hangs at "exporting to image", press Ctrl+C
# The image will still be created and tagged automatically
./docker-build.sh
```

### Container Logs
```bash
# View logs from mounted directory
docker run -v ./logs:/app/logs redb:latest python3 start.py --path /samples
tail -f logs/*.txt
```

## Production Notes

### Resource Requirements
- **Memory**: 2-4GB recommended (8GB for decompilation)
- **CPU**: 2+ cores recommended
- **Disk**: Minimal (stateless container)
- **Network**: Access to ClickHouse and S3 services

### Security
- Container runs as non-root user `analyzer` (UID 1000)
- Sample files should be mounted read-only
- No persistent state between container runs
- Isolated processing environment for malware analysis

### Deployment Architecture

This container is designed for:
- **Nomad job dispatch**: Single-use containers processing one sample each
- **Kubernetes jobs**: Batch processing with external orchestration
- **CI/CD pipelines**: Automated analysis in build systems
- **Development**: Local testing and debugging

The unified container approach means the same image handles both feature extraction and decompilation - the difference is only in the command-line flags used when starting the container.