README.md

NiChart: Neuro-imaging Chart

NiChart is a comprehensive framework designed to revolutionize neuroimaging research. It offers large-scale neuroimaging capabilities, sophisticated analysis methods, and user-friendly tools, all seamlessly integrated into a local installation version and the AWS Cloud.

Components

1. Image Processing: Utilizes tools like DLMUSE, fMRIPrep XCEPengine, and QSIPrep for effective image analytics.
2. Reference Data Curation: Houses ISTAGING, 70000 Scans, and 14 individual studies to provide curated reference data.
3. Data Harmonization: Employs neuroharmonize and Combat for ensuring consistent data standards.
4. Machine Learning Models: Provides Supervised, Semi-supervised, and DL Models for advanced neuroimaging analysis including SpareScore.
5. Data Visualization: Features like Centile curves, direct image linking, and reference values for comprehensive data visualization.
6. Deployment: Supports open-source Github components and Docker container compatibility deployed in a local environment & AWS Cloud.

System Requirements

For recommended system configuration, please refer to: nnUNet hardware requirements.

Installation Instructions

1. Mamba installation Mamba Installation Guide (Official)

   Example (Linux x86):

   wget https://github.com/conda-forge/miniforge/releases/latest/download/Mambaforge-Linux-x86_64.sh
   
   bash Mambaforge-Linux-x86_64.sh
   mamba create -c conda-forge -c bioconda -n NCP_env python=3.12 snakemake
   mamba activate NCP_env

2. Manual installation

   git clone https://github.com/CBICA/NiChart_Project.git
   pip install -r requirements.txt

Run NiChart Locally (GUI)

cd src/viewer/
streamlit run NiChartProject.py

The app will start in your localhost.

Quick Links

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