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--== **Overview** ==
++**# Neurodiagnoses AI: Multimodal AI for Neurodiagnostic Predictions**
--Neurodiagnoses develops a **tridimensional diagnostic framework** for **CNS diseases**, incorporating **AI-powered annotation tools** to improve **interpretability, standardization, and clinical utility.**
++## **Project Overview**
++Neurodiagnoses AI implements AI-driven diagnostic and prognostic models for central nervous system (CNS) disorders, adapting the Florey Dementia Index (FDI) methodology to a broader set of neurological conditions. The approach integrates **multimodal data sources** (EEG, neuroimaging, biomarkers, and genetics) and employs **machine learning models** to provide **explainable, real-time diagnostic insights**.##
--This methodology integrates **multi-modal data**, including:
--**Genetic data** (whole-genome sequencing, polygenic risk scores).
--**Neuroimaging** (MRI, PET, EEG, MEG).
--**Neurophysiological data** (EEG-based biomarkers, sleep actigraphy).
--**CSF & Blood Biomarkers** (Amyloid-beta, Tau, Neurofilament Light).
++## **How to Use External Databases in Neurodiagnoses**
++To enhance diagnostic accuracy, Neurodiagnoses integrates data from multiple biomedical and neurological research databases. Researchers can follow these steps to access, prepare, and integrate data into the Neurodiagnoses framework.##
--By applying **machine learning models**, Neurodiagnoses generates **structured, explainable diagnostic outputs** to assist **clinical decision-making** and **biomarker-driven patient stratification.**
++### **Potential Data Sources**
++Neurodiagnoses maintains an updated list of potential biomedical databases relevant to neurodegenerative diseases. ##
------
++**Reference: List of Potential Databases**
++- **ADNI**: Alzheimer's Disease data ([ADNI](https://adni.loni.usc.edu))
++- **PPMI**: Parkinson’s Disease Imaging and biospecimens ([PPMI](https://www.ppmi-info.org))
++- **GP2**: Whole-genome sequencing for PD ([GP2](https://gp2.org))
++- **Enroll-HD**: Huntington’s Disease Clinical and genetic data ([Enroll-HD](https://www.enroll-hd.org))
++- **GAAIN**: Multi-source Alzheimer’s data aggregation ([GAAIN](https://gaain.org))
++- **UK Biobank**: Population-wide genetic, imaging, and health records ([UK Biobank](https://www.ukbiobank.ac.uk))
++- **DPUK**: Dementia and Aging data ([DPUK](https://www.dementiasplatform.uk))
++- **PRION Registry**: Prion Diseases clinical and genetic data ([PRION Registry](https://prionregistry.org))
++- **DECIPHER**: Rare genetic disorder genomic variants ([DECIPHER](https://decipher.sanger.ac.uk))
--== **Data Integration & External Databases** ==
++### **1. Register for Access**
++- Each external database requires **individual registration** and access approval.
++- Ensure compliance with **ethical approvals** and **data usage agreements** before integrating datasets into Neurodiagnoses.
++- Some repositories may require a **Data Usage Agreement (DUA)** for sensitive medical data.##
--=== **How to Use External Databases in Neurodiagnoses** ===
++### **2. Download & Prepare Data**
++- Download datasets while adhering to database usage policies.
++- Ensure files meet **Neurodiagnoses format requirements**:
++  - **Tabular Data**: `.csv`, `.tsv`
++  - **Neuroimaging Data**: `.nii`, `.dcm`
++  - **Genomic Data**: `.fasta`, `.vcf`
++  - **Clinical Metadata**: `.json`, `.xml`##
--Neurodiagnoses integrates data from multiple **biomedical and neurological research databases**. Researchers can follow these steps to **access, prepare, and integrate** data into the Neurodiagnoses framework.
++- **Mandatory Fields for Integration**:
++  - **Subject ID**: Unique patient identifier
++  - **Diagnosis**: Standardized disease classification
++  - **Biomarkers**: CSF, plasma, or imaging biomarkers
++  - **Genetic Data**: Whole-genome or exome sequencing
++  - **Neuroimaging Metadata**: MRI/PET acquisition parameters
--**Potential Data Sources**
--**Reference:** [[List of Potential Databases>>url:https://github.com/Fundacion-de-Neurociencias/neurodiagnoses/blob/main/data/sources/list_of_potential_databases]]
++### **3. Upload Data to Neurodiagnoses**
++**Option 1: Upload to EBRAINS Bucket**
++- Location: **EBRAINS Neurodiagnoses Bucket**
++- Ensure correct **metadata tagging** before submission.##
--=== **Register for Access** ===
++ **Option 2: Contribute via GitHub Repository**
++- Location: **GitHub Data Repository**
++- Create a new folder under `/data/` and include a **dataset description**.
++- For large datasets, contact project administrators before uploading.
--Each **external database** requires **individual registration** and approval.
--✔️ Follow the official **data access guidelines** of each provider.
--✔️ Ensure compliance with **ethical approvals** and **data-sharing agreements (DUAs).**
++### **4. Integrate Data into AI Models**
++- Open **Jupyter Notebooks** on EBRAINS to run **preprocessing scripts**.
++- Standardize **neuroimaging and biomarker formats** using harmonization tools.
++- Use **machine learning models** to handle missing data and feature extraction.
++- Train AI models with **newly integrated patient cohorts**.##
--=== **Download & Prepare Data** ===
++**Reference**: See `docs/data_processing.md` for detailed instructions.
--Once access is granted, download datasets **following compliance guidelines** and **format requirements** for integration.
++## **Collaboration & Partnerships**##
++# **Partnering with Data Providers**
++Neurodiagnoses seeks partnerships with data repositories to:
++- Enable **API-based data integration** for real-time processing.
++- Co-develop **harmonized AI-ready datasets** with standardized annotations.
++- Secure **funding opportunities** through joint grant applications.
--**Supported File Formats**
++**Interested in Partnering?**
++- If you represent a research consortium or database provider, reach out to explore data-sharing agreements.
++- **Contact**: info@neurodiagnoses.com
--* **Tabular Data**: .csv, .tsv
--* **Neuroimaging Data**: .nii, .dcm
--* **Genomic Data**: .fasta, .vcf
--* **Clinical Metadata**: .json, .xml
++## **Final Notes**
++Neurodiagnoses continuously expands its data ecosystem to support AI-driven clinical decision-making. Researchers and institutions are encouraged to contribute **new datasets and methodologies**.##
--**Mandatory Fields for Integration**
++For additional technical documentation:
++- **GitHub Repository**: [Neurodiagnoses GitHub](https://github.com/neurodiagnoses)
++- **EBRAINS Collaboration Page**: [EBRAINS Neurodiagnoses](https://ebrains.eu/collabs/neurodiagnoses)
--|=**Field Name**|=**Description**
--|**Subject ID**|Unique patient identifier
--|**Diagnosis**|Standardized disease classification
--|**Biomarkers**|CSF, plasma, or imaging biomarkers
--|**Genetic Data**|Whole-genome or exome sequencing
--|**Neuroimaging Metadata**|MRI/PET acquisition parameters
++If you experience issues integrating data, **open a GitHub Issue** or consult the **EBRAINS Neurodiagnoses Forum**.
--=== **Upload Data to Neurodiagnoses** ===
++== **How to Use External Databases in Neurodiagnoses** ==
--**Option 1:** Upload to **EBRAINS Bucket** → [[Neurodiagnoses Data Storage>>url:https://wiki.ebrains.eu/bin/view/Collabs/neurodiagnoses/Bucket]]
--**Option 2:** Contribute via **GitHub Repository** → [[GitHub Data Repository>>url:https://github.com/Fundacion-de-Neurociencias/neurodiagnoses/tree/main/data]]
++To enhance the accuracy of our diagnostic models, Neurodiagnoses integrates data from multiple biomedical and neurological research databases. If you are a researcher, follow these steps to access, prepare, and integrate data into the Neurodiagnoses framework.
--**For large datasets, please contact project administrators before uploading.**
++=== **Potential Data Sources** ===
--=== **Integrate Data into AI Models** ===
++Neurodiagnoses maintains an updated list of potential biomedical databases relevant to neurodegenerative diseases.
--Use **Jupyter Notebooks** on EBRAINS for **data preprocessing.**
--Standardize data using **harmonization tools.**
--Train AI models with **newly integrated datasets.**
++* Reference: [[List of Potential Databases>>url:https://github.com/Fundacion-de-Neurociencias/neurodiagnoses/blob/main/data/sources/list_of_potential_databases]]
--**Reference:** [[Data Processing Guide>>url:https://github.com/Fundacion-de-Neurociencias/neurodiagnoses/blob/main/docs/data_processing.md]]
++=== **1. Register for Access** ===
------
++Each external database requires individual registration and access approval. Follow the official guidelines of each database provider.
--== **AI-Powered Annotation & Machine Learning Models** ==
++* Ensure that you have completed all ethical approvals and data access agreements before integrating datasets into Neurodiagnoses.
++* Some repositories require a Data Usage Agreement (DUA) before downloading sensitive medical data.
--Neurodiagnoses applies **advanced machine learning models** to classify CNS diseases, extract features from **biomarkers and neuroimaging**, and provide **AI-powered annotation.**
++=== **2. Download & Prepare Data** ===
--=== **AI Model Categories** ===
++Once access is granted, download datasets while complying with data usage policies. Ensure that the files meet Neurodiagnoses’ format requirements for smooth integration.
--|=**Model Type**|=**Function**|=**Example Algorithms**
--|**Probabilistic Diagnosis**|Assigns probability scores to multiple CNS disorders.|Random Forest, XGBoost, Bayesian Networks
--|**Tridimensional Diagnosis**|Classifies disorders based on Etiology, Biomarkers, and Neuroanatomical Correlations.|CNNs, Transformers, Autoencoders
--|**Biomarker Prediction**|Predicts missing biomarker values using regression.|KNN Imputation, Bayesian Estimation
--|**Neuroimaging Feature Extraction**|Extracts patterns from MRI, PET, EEG.|CNNs, Graph Neural Networks
--|**Clinical Decision Support**|Generates AI-driven diagnostic reports.|SHAP Explainability Tools
++==== **Supported File Formats** ====
--**Reference:** [[AI Model Documentation>>url:https://github.com/Fundacion-de-Neurociencias/neurodiagnoses/blob/main/docs/models.md]]
++* Tabular Data: .csv, .tsv
++* Neuroimaging Data: .nii, .dcm
++* Genomic Data: .fasta, .vcf
++* Clinical Metadata: .json, .xml
------
++==== **Mandatory Fields for Integration** ====
--== **Clinical Decision Support & Tridimensional Diagnostic Framework** ==
++|=Field Name|=Description
++|Subject ID|Unique patient identifier
++|Diagnosis|Standardized disease classification
++|Biomarkers|CSF, plasma, or imaging biomarkers
++|Genetic Data|Whole-genome or exome sequencing
++|Neuroimaging Metadata|MRI/PET acquisition parameters
--Neurodiagnoses generates **structured AI reports** for clinicians, combining:
++=== **3. Upload Data to Neurodiagnoses** ===
--**Probabilistic Diagnosis:** AI-generated ranking of potential diagnoses.
--**Tridimensional Classification:** Standardized diagnostic reports based on:
++Once preprocessed, data can be uploaded to EBRAINS or GitHub.
--1. **Axis 1:** **Etiology** → Genetic, Autoimmune, Prion, Toxic, Vascular.
--1. **Axis 2:** **Molecular Markers** → CSF, Neuroinflammation, EEG biomarkers.
--1. **Axis 3:** **Neuroanatomoclinical Correlations** → MRI atrophy, PET.
++* (((
++**Option 1: Upload to EBRAINS Bucket**
--**Reference:** [[Tridimensional Classification Guide>>url:https://github.com/Fundacion-de-Neurociencias/neurodiagnoses/blob/main/docs/classification.md]]
++* Location: [[EBRAINS Neurodiagnoses Bucket>>url:https://wiki.ebrains.eu/bin/view/Collabs/neurodiagnoses/Bucket]]
++* Ensure correct metadata tagging before submission.
++)))
++* (((
++**Option 2: Contribute via GitHub Repository**
------
++* Location: [[GitHub Data Repository>>url:https://github.com/Fundacion-de-Neurociencias/neurodiagnoses/tree/main/data]]
++* Create a new folder under /data/ and include dataset description.
++)))
--== **Data Security, Compliance & Federated Learning** ==
++//Note: For large datasets, please contact the project administrators before uploading.//
--✔ **Privacy-Preserving AI**: Implements **Federated Learning**, ensuring that patient data **never leaves** local institutions.
--✔ **Secure Data Access**: Data remains **stored in EBRAINS MIP servers** using **differential privacy techniques.**
--✔ **Ethical & GDPR Compliance**: Data-sharing agreements **must be signed** before use.
++=== **4. Integrate Data into AI Models** ===
--**Reference:** [[Data Protection & Federated Learning>>url:https://github.com/Fundacion-de-Neurociencias/neurodiagnoses/blob/main/docs/security.md]]
++Once uploaded, datasets must be harmonized and formatted before AI model training.
------
++==== **Steps for Data Integration** ====
--== **Data Processing & Integration with Clinica.Run** ==
++* Open Jupyter Notebooks on EBRAINS to run preprocessing scripts.
++* Standardize neuroimaging and biomarker formats using harmonization tools.
++* Use machine learning models to handle missing data and feature extraction.
++* Train AI models with newly integrated patient cohorts.
++* Reference: [[Detailed instructions can be found in docs/data_processing.md>>url:https://github.com/Fundacion-de-Neurociencias/neurodiagnoses/blob/main/docs/data_processing.md]].
--Neurodiagnoses now supports **Clinica.Run**, an **open-source neuroimaging platform** for **multimodal data processing.**
++----
--=== **How It Works** ===
++== **Database Sources Table** ==
--✔ **Neuroimaging Preprocessing**: MRI, PET, EEG data is preprocessed using **Clinica.Run pipelines.**
--✔ **Automated Biomarker Extraction**: Extracts volumetric, metabolic, and functional biomarkers.
--✔ **Data Security & Compliance**: Clinica.Run is **GDPR & HIPAA-compliant.**
++=== **Where to Insert This** ===
--=== **Implementation Steps** ===
++* GitHub: [[docs/data_sources.md>>url:https://github.com/Fundacion-de-Neurociencias/neurodiagnoses/blob/main/docs/data_sources.md]]
++* EBRAINS Wiki: Collabs/neurodiagnoses/Data Sources
--1. Install **Clinica.Run** dependencies.
--1. Configure **Clinica.Run pipeline** in clinica_run_config.json.
--1. Run **biomarker extraction pipelines** for AI-based diagnostics.
++=== **Key Databases for Neurodiagnoses** ===
--**Reference:** [[Clinica.Run Documentation>>url:https://github.com/Fundacion-de-Neurociencias/neurodiagnoses/blob/main/docs/clinica_run.md]]
++|=Database|=Focus Area|=Data Type|=Access Link
++|ADNI|Alzheimer's Disease|MRI, PET, CSF, cognitive tests|ADNI
++|PPMI|Parkinson’s Disease|Imaging, biospecimens|[[PPMI>>url:https://www.ppmi-info.org/]]
++|GP2|Genetic Data for PD|Whole-genome sequencing|[[GP2>>url:https://gp2.org/]]
++|Enroll-HD|Huntington’s Disease|Clinical, genetic, imaging|[[Enroll-HD>>url:https://enroll-hd.org/]]
++|GAAIN|Alzheimer's & Cognitive Decline|Multi-source data aggregation|[[GAAIN>>url:https://www.gaain.org/]]
++|UK Biobank|Population-wide studies|Genetic, imaging, health records|[[UK Biobank>>url:https://www.ukbiobank.ac.uk/]]
++|DPUK|Dementia & Aging|Imaging, genetics, lifestyle factors|[[DPUK>>url:https://www.dementiasplatform.uk/]]
++|PRION Registry|Prion Diseases|Clinical and genetic data|[[PRION Registry>>url:https://www.prionalliance.org/]]
++|DECIPHER|Rare Genetic Disorders|Genomic variants|DECIPHER
++If you know a relevant dataset, submit a proposal in [[GitHub Issues>>url:https://github.com/Fundacion-de-Neurociencias/neurodiagnoses/issues]].
++
  ----
--== **Collaborative Development & Research** ==
++== **Collaboration & Partnerships** ==
--**We Use GitHub to Develop AI Models & Store Research Data**
++=== **Where to Insert This** ===
--* **GitHub Repository:** AI model training scripts.
--* **GitHub Issues:** Tracks ongoing research questions.
--* **GitHub Wiki:** Project documentation & user guides.
++* GitHub: [[docs/collaboration.md>>url:https://github.com/Fundacion-de-Neurociencias/neurodiagnoses/blob/main/docs/collaboration.md]]
++* EBRAINS Wiki: Collabs/neurodiagnoses/Collaborations
--**We Use EBRAINS for Data & Collaboration**
++=== **Partnering with Data Providers** ===
--* **EBRAINS Buckets:** Large-scale neuroimaging and biomarker storage.
--* **EBRAINS Jupyter Notebooks:** Cloud-based AI model execution.
--* **EBRAINS Wiki:** Research documentation and updates.
++Beyond using existing datasets, Neurodiagnoses seeks partnerships with data repositories to:
--**Join the Project Forum:** [[GitHub Discussions>>url:https://github.com/Fundacion-de-Neurociencias/neurodiagnoses/discussions]]
++* Enable direct API-based data integration for real-time processing.
++* Co-develop harmonized AI-ready datasets with standardized annotations.
++* Secure funding opportunities through joint grant applications.
------
++=== **Interested in Partnering?** ===
--**For Additional Documentation:**
++If you represent a research consortium or database provider, reach out to explore data-sharing agreements.
--* **GitHub Repository:** [[Neurodiagnoses AI Models>>url:https://github.com/Fundacion-de-Neurociencias/neurodiagnoses]]
--* **EBRAINS Wiki:** [[Neurodiagnoses Research Collaboration>>url:https://wiki.ebrains.eu/bin/view/Collabs/neurodiagnoses/]]
++* Contact: [[info@neurodiagnoses.com>>mailto:info@neurodiagnoses.com]]
  ----
--**Neurodiagnoses is Open for Contributions – Join Us Today!**
++== **Final Notes** ==
++
++Neurodiagnoses continuously expands its data ecosystem to support AI-driven clinical decision-making. Researchers and institutions are encouraged to contribute new datasets and methodologies.
++
++For additional technical documentation:
++
++* [[GitHub Repository>>url:https://github.com/Fundacion-de-Neurociencias/neurodiagnoses]]
++* [[EBRAINS Collaboration Page>>url:https://wiki.ebrains.eu/bin/view/Collabs/neurodiagnoses/]]
++
++If you experience issues integrating data, open a [[GitHub Issue>>url:https://github.com/Fundacion-de-Neurociencias/neurodiagnoses/issues]] or consult the EBRAINS Neurodiagnoses Forum.