DICOM to NIfTI Converter with AWS Visualization

This project converts DICOM files to NIfTI format and provides visualization capabilities using AWS services.

Basic Setup (DICOM Conversion)

Step 1: Install Required Libraries

pip install -r requirements.txt

Step 2: Generate Sample Data

python data_generator.py

Generated data will be in: data/raw_dicoms

Step 3: Run Converter

python main.py

Converted data will be in: data/bids_output

AWS Visualization Setup

Step 1: Install AWS Tools

pip install boto3 streamlit

Step 2: Set Up AWS Credentials

1. Get your AWS credentials

   • Log into AWS Console
   • Click your name in top right
   • Click "Security credentials"
   • Create new access key
   • Save both the Access Key ID and Secret Access Key

2. Set up credentials on your computer

# Option 1: Set environment variables
export AWS_ACCESS_KEY_ID='your-key-here'
export AWS_SECRET_ACCESS_KEY='your-secret-here'

# Option 2: Create AWS credentials file
mkdir ~/.aws
touch ~/.aws/credentials

Then add to credentials file:

[default]
aws_access_key_id = your-key-here
aws_secret_access_key = your-secret-here

Step 3: Run the Visualization

streamlit run visualization_app.py

Then open your browser to: http://localhost:8501

How It Works

Step 1: DICOM Processing
Your DICOM Files → Convert to NIfTI → Save Locally

Step 2: AWS Storage
Local Files → Upload to AWS → Safe Storage in the Cloud

Step 3: Visualization
Cloud Data → Process → Show Pretty Charts

Data Flow Diagram

DICOM Files
    ↓
Data Generator
    ↓
Converter
    ↓
AWS Upload
    ↓
Visualization