diff --git a/README.md b/README.md index a2d7f49..12601af 100644 --- a/README.md +++ b/README.md @@ -6,61 +6,24 @@ reference distributions for comparison to a broader population. ![NiChart flowchart](resources/images/NiChart_Flowchart_v2.svg) -We provide both locally deployable software and a cloud application. [NiChart cloud application](https://neuroimagingchart.com/portal), hosted via Amazon Web Services (AWS), deploys -scalable infrastructure which hosts the NiChart tools as a standard web application accessible via the user’s web browser. The cloud and desktop applications are unified at the code level through the use of the Python library [Streamlit](https://streamlit.io/). Consequently, the user experience is nearly completely identical between the cloud and desktop applications. - -## Components - -1. **Image Processing**: Utilizes tools like [DLMUSE](https://github.com/CBICA/NiChart_DLMUSE), [fMRIPrep](https://github.com/nipreps/fmriprep) [XCEPengine](https://github.com/PennLINC/xcp_d), and [QSIPrep](https://github.com/PennLINC/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](https://github.com/rpomponio/neuroHarmonize) and [Combat](https://github.com/Zheng206/ComBatFam_Pipeline) for ensuring consistent data standards. -4. **Machine Learning Models**: Provides Supervised, Semi-supervised, and DL Models for advanced neuroimaging analysis including [SpareScore](https://github.com/CBICA/spare_score). -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](https://aws.amazon.com/). +# Main Goals: +The development of nichart is guided by several core principles: -## System Requirements +1. Enabling near real-time image processing and analysis through advanced methods. -For recommended system configuration, please refer to: [nnUNet hardware requirements](https://github.com/MIC-DKFZ/nnUNet/blob/master/documentation/installation_instructions.md#hardware-requirements). +2. Integrating cutting-edge methods and enabling the continuous integration of new processing and analysis techniques to extract meaningful AI biomarkers from multi-modal neuroimaging data. -## Installation Instructions +3. Ensuring robust and reliable results through extensive data training and validation on large and diverse training datasets. -1. (Optional but recommended for environment management) Mamba installation - [Mamba Installation Guide (Official)](https://mamba.readthedocs.io/en/latest/installation/mamba-installation.html) +4. Providing user-friendly tools for result visualization and reporting. - Example (Linux x86): - ```bash - wget https://github.com/conda-forge/miniforge/releases/latest/download/Mambaforge-Linux-x86_64.sh +5. Developing a deployment strategy that enables easy access for users with varying technical expertise and hardware resources. - bash Mambaforge-Linux-x86_64.sh - mamba create -c conda-forge -c bioconda -n NCP_env python=3.12 - mamba activate NCP_env - ``` -2. Install NiChart_Project into the environment - ```bash - git clone https://github.com/CBICA/NiChart_Project.git - pip install -r requirements.txt - ``` +# Running NiChart: -3. Install the proper PyTorch version for your device - Numpy and PyTorch have some compatibility issues which have changed variously on different platforms. To avoid frustration with these issues, please install PyTorch as noted below. - - After installing all other requirements, uninstall Torch: - ``` - pip uninstall torch - ``` - - Then install PyTorch using the following command. Make sure to use the correct index url for your CUDA version as specified on the [PyTorch getting started page](https://pytorch.org/get-started/locally/). - On Linux, use version 2.3.1. On Windows, 2.5.1 is known to work. - ``` - pip install torch==2.3.1 --index-url https://download.pytorch.org/whl/cu121 - ``` -## Run NiChart Locally (GUI) -```bash -cd src/viewer/ -streamlit run NiChartProject.py -``` -The app will start in your localhost. +We provide both a locally deployable desktop application and a cloud application. For the desktop application please see [FIXME: link to readthedocs and Github]. [NiChart cloud application](https://neuroimagingchart.com/portal), hosted via Amazon Web Services (AWS), deploys +scalable infrastructure which hosts the NiChart tools as a standard web application accessible via the user’s web browser. The cloud and desktop applications are unified at the code level through the use of the Python library [Streamlit](https://streamlit.io/). Consequently, the user experience is nearly completely identical between the cloud and desktop applications. ## Quick Links diff --git a/docs2/usage.rst b/docs2/usage.rst index 622f5dd..64f28a7 100644 --- a/docs2/usage.rst +++ b/docs2/usage.rst @@ -18,10 +18,10 @@ The following steps describe how to run NiChart after installation: :: Cloud ***** -The cloud app can be launched at https://cloud.neuroimagingchart.com . Users need to create an account to access the cloud app. +The cloud app can be launched at https://cloud.neuroimagingchart.com . Users need to create an account and login to access the cloud app. ***** Usage ***** -After launching the application, users can select a pipeline and apply it to their data. For detailed instructions on each pipeline, please refer to the **Overview** and **Tutorial** pages accessible from the left-hand menu. +After launching the application, users can select a pipeline and apply it to their data. For detailed instructions on each pipeline, please refer to the **Pipeline Overview** and **Tutorial** pages accessible from the left-hand menu.