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1	1	== **Overview** ==
2	2
3		-Neurodiagnoses develops a **tridimensional diagnostic framework** for **CNS diseases**, incorporating **AI-powered annotation tools** to improve **interpretability, standardization, and clinical utility.**
	3	+Neurodiagnoses develops a tridimensional diagnostic framework for CNS diseases, incorporating AI-powered annotation tools to improve interpretability, standardization, and clinical utility. The methodology integrates multi-modal data, including genetic, neuroimaging, neurophysiological, and biomarker datasets, and applies machine learning models to generate structured, explainable diagnostic outputs.
4	4
5		-This methodology integrates **multi-modal data**, including:
6		-**Genetic data** (whole-genome sequencing, polygenic risk scores).
7		-**Neuroimaging** (MRI, PET, EEG, MEG).
8		-**Neurophysiological data** (EEG-based biomarkers, sleep actigraphy).
9		-**CSF & Blood Biomarkers** (Amyloid-beta, Tau, Neurofilament Light).
10		-
11		-By applying **machine learning models**, Neurodiagnoses generates **structured, explainable diagnostic outputs** to assist **clinical decision-making** and **biomarker-driven patient stratification.**
12		-
13	13	----
14	14
15		-== **Data Integration & External Databases** ==
	7	+== **How to Use External Databases in Neurodiagnoses** ==
16	16
17		-=== **How to Use External Databases in Neurodiagnoses** ===
	9	+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.
18	18
19		-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.
	11	+=== **Potential Data Sources** ===
20	20
21		-**Potential Data Sources**
22		-**Reference:** [[List of Potential Databases>>url:https://github.com/Fundacion-de-Neurociencias/neurodiagnoses/blob/main/data/sources/list_of_potential_databases]]
	13	+Neurodiagnoses maintains an updated list of potential biomedical databases relevant to neurodegenerative diseases.
23	23
24		-=== **Register for Access** ===
	15	+* Reference: [[List of Potential Databases>>url:https://github.com/Fundacion-de-Neurociencias/neurodiagnoses/blob/main/data/sources/list_of_potential_databases]]
25	25
26		-Each **external database** requires **individual registration** and approval.
27		-✔️ Follow the official **data access guidelines** of each provider.
28		-✔️ Ensure compliance with **ethical approvals** and **data-sharing agreements (DUAs).**
	17	+=== **1. Register for Access** ===
29	29
30		-=== **Download & Prepare Data** ===
	19	+Each external database requires individual registration and access approval. Follow the official guidelines of each database provider.
31	31
32		-Once access is granted, download datasets **following compliance guidelines** and **format requirements** for integration.
	21	+* Ensure that you have completed all ethical approvals and data access agreements before integrating datasets into Neurodiagnoses.
	22	+* Some repositories require a Data Usage Agreement (DUA) before downloading sensitive medical data.
33	33
34		-**Supported File Formats**
	24	+=== **2. Download & Prepare Data** ===
35	35
36		-* **Tabular Data**: .csv, .tsv
37		-* **Neuroimaging Data**: .nii, .dcm
38		-* **Genomic Data**: .fasta, .vcf
39		-* **Clinical Metadata**: .json, .xml
	26	+Once access is granted, download datasets while complying with data usage policies. Ensure that the files meet Neurodiagnoses’ format requirements for smooth integration.
40	40
41		-**Mandatory Fields for Integration**
	28	+==== **Supported File Formats** ====
42	42
43		-|=**Field Name**|=**Description**
44		-|**Subject ID**|Unique patient identifier
45		-|**Diagnosis**|Standardized disease classification
46		-|**Biomarkers**|CSF, plasma, or imaging biomarkers
47		-|**Genetic Data**|Whole-genome or exome sequencing
48		-|**Neuroimaging Metadata**|MRI/PET acquisition parameters
	30	+* Tabular Data: .csv, .tsv
	31	+* Neuroimaging Data: .nii, .dcm
	32	+* Genomic Data: .fasta, .vcf
	33	+* Clinical Metadata: .json, .xml
49	49
50		-=== **Upload Data to Neurodiagnoses** ===
	35	+==== **Mandatory Fields for Integration** ====
51	51
52		-**Option 1:** Upload to **EBRAINS Bucket** → [[Neurodiagnoses Data Storage>>url:https://wiki.ebrains.eu/bin/view/Collabs/neurodiagnoses/Bucket]]
53		-**Option 2:** Contribute via **GitHub Repository** → [[GitHub Data Repository>>url:https://github.com/Fundacion-de-Neurociencias/neurodiagnoses/tree/main/data]]
	37	+|=Field Name|=Description
	38	+|Subject ID|Unique patient identifier
	39	+|Diagnosis|Standardized disease classification
	40	+|Biomarkers|CSF, plasma, or imaging biomarkers
	41	+|Genetic Data|Whole-genome or exome sequencing
	42	+|Neuroimaging Metadata|MRI/PET acquisition parameters
54	54
55		-**For large datasets, please contact project administrators before uploading.**
	44	+=== **3. Upload Data to Neurodiagnoses** ===
56	56
57		-=== **Integrate Data into AI Models** ===
	46	+Once preprocessed, data can be uploaded to EBRAINS or GitHub.
58	58
59		-Use **Jupyter Notebooks** on EBRAINS for **data preprocessing.**
60		-Standardize data using **harmonization tools.**
61		-Train AI models with **newly integrated datasets.**
	48	+* (((
	49	+**Option 1: Upload to EBRAINS Bucket**
62	62
63		-**Reference:** [[Data Processing Guide>>url:https://github.com/Fundacion-de-Neurociencias/neurodiagnoses/blob/main/docs/data_processing.md]]
	51	+* Location: [[EBRAINS Neurodiagnoses Bucket>>url:https://wiki.ebrains.eu/bin/view/Collabs/neurodiagnoses/Bucket]]
	52	+* Ensure correct metadata tagging before submission.
	53	+)))
	54	+* (((
	55	+**Option 2: Contribute via GitHub Repository**
64	64
65		-----
	57	+* Location: [[GitHub Data Repository>>url:https://github.com/Fundacion-de-Neurociencias/neurodiagnoses/tree/main/data]]
	58	+* Create a new folder under /data/ and include dataset description.
	59	+)))
66	66
67		-== **AI-Powered Annotation & Machine Learning Models** ==
	61	+//Note: For large datasets, please contact the project administrators before uploading.//
68	68
69		-Neurodiagnoses applies **advanced machine learning models** to classify CNS diseases, extract features from **biomarkers and neuroimaging**, and provide **AI-powered annotation.**
	63	+=== **4. Integrate Data into AI Models** ===
70	70
71		-=== **AI Model Categories** ===
	65	+Once uploaded, datasets must be harmonized and formatted before AI model training.
72	72
73		-|=**Model Type**|=**Function**|=**Example Algorithms**
74		-|**Probabilistic Diagnosis**|Assigns probability scores to multiple CNS disorders.|Random Forest, XGBoost, Bayesian Networks
75		-|**Tridimensional Diagnosis**|Classifies disorders based on Etiology, Biomarkers, and Neuroanatomical Correlations.|CNNs, Transformers, Autoencoders
76		-|**Biomarker Prediction**|Predicts missing biomarker values using regression.|KNN Imputation, Bayesian Estimation
77		-|**Neuroimaging Feature Extraction**|Extracts patterns from MRI, PET, EEG.|CNNs, Graph Neural Networks
78		-|**Clinical Decision Support**|Generates AI-driven diagnostic reports.|SHAP Explainability Tools
	67	+==== **Steps for Data Integration** ====
79	79
80		-**Reference:** [[AI Model Documentation>>url:https://github.com/Fundacion-de-Neurociencias/neurodiagnoses/blob/main/docs/models.md]]
	69	+* Open Jupyter Notebooks on EBRAINS to run preprocessing scripts.
	70	+* Standardize neuroimaging and biomarker formats using harmonization tools.
	71	+* Use machine learning models to handle missing data and feature extraction.
	72	+* Train AI models with newly integrated patient cohorts.
	73	+* 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]].
81	81
82	82	----
83	83
84		-== **Clinical Decision Support & Tridimensional Diagnostic Framework** ==
	77	+== **Database Sources Table** ==
85	85
86		-Neurodiagnoses generates **structured AI reports** for clinicians, combining:
	79	+=== **Where to Insert This** ===
87	87
88		-**Probabilistic Diagnosis:** AI-generated ranking of potential diagnoses.
89		-**Tridimensional Classification:** Standardized diagnostic reports based on:
	81	+* GitHub: [[docs/data_sources.md>>url:https://github.com/Fundacion-de-Neurociencias/neurodiagnoses/blob/main/docs/data_sources.md]]
	82	+* EBRAINS Wiki: Collabs/neurodiagnoses/Data Sources
90	90
91		-1. **Axis 1:** **Etiology** → Genetic, Autoimmune, Prion, Toxic, Vascular.
92		-1. **Axis 2:** **Molecular Markers** → CSF, Neuroinflammation, EEG biomarkers.
93		-1. **Axis 3:** **Neuroanatomoclinical Correlations** → MRI atrophy, PET.
	84	+=== **Key Databases for Neurodiagnoses** ===
94	94
95		-**Reference:** [[Tridimensional Classification Guide>>url:https://github.com/Fundacion-de-Neurociencias/neurodiagnoses/blob/main/docs/classification.md]]
	86	+|=Database|=Focus Area|=Data Type|=Access Link
	87	+|ADNI|Alzheimer's Disease|MRI, PET, CSF, cognitive tests|ADNI
	88	+|PPMI|Parkinson’s Disease|Imaging, biospecimens|[[PPMI>>url:https://www.ppmi-info.org/]]
	89	+|GP2|Genetic Data for PD|Whole-genome sequencing|[[GP2>>url:https://gp2.org/]]
	90	+|Enroll-HD|Huntington’s Disease|Clinical, genetic, imaging|[[Enroll-HD>>url:https://enroll-hd.org/]]
	91	+|GAAIN|Alzheimer's & Cognitive Decline|Multi-source data aggregation|[[GAAIN>>url:https://www.gaain.org/]]
	92	+|UK Biobank|Population-wide studies|Genetic, imaging, health records|[[UK Biobank>>url:https://www.ukbiobank.ac.uk/]]
	93	+|DPUK|Dementia & Aging|Imaging, genetics, lifestyle factors|[[DPUK>>url:https://www.dementiasplatform.uk/]]
	94	+|PRION Registry|Prion Diseases|Clinical and genetic data|[[PRION Registry>>url:https://www.prionalliance.org/]]
	95	+|DECIPHER|Rare Genetic Disorders|Genomic variants|DECIPHER
96	96
97		-----
	97	+If you know a relevant dataset, submit a proposal in [[GitHub Issues>>url:https://github.com/Fundacion-de-Neurociencias/neurodiagnoses/issues]].
98	98
99		-== **Data Security, Compliance & Federated Learning** ==
100		-
101		-✔ **Privacy-Preserving AI**: Implements **Federated Learning**, ensuring that patient data **never leaves** local institutions.
102		-✔ **Secure Data Access**: Data remains **stored in EBRAINS MIP servers** using **differential privacy techniques.**
103		-✔ **Ethical & GDPR Compliance**: Data-sharing agreements **must be signed** before use.
104		-
105		-**Reference:** [[Data Protection & Federated Learning>>url:https://github.com/Fundacion-de-Neurociencias/neurodiagnoses/blob/main/docs/security.md]]
106		-
107	107	----
108	108
109		-== **Data Processing & Integration with Clinica.Run** ==
	101	+== **Collaboration & Partnerships** ==
110	110
111		-Neurodiagnoses now supports **Clinica.Run**, an **open-source neuroimaging platform** for **multimodal data processing.**
	103	+=== **Where to Insert This** ===
112	112
113		-=== **How It Works** ===
	105	+* GitHub: [[docs/collaboration.md>>url:https://github.com/Fundacion-de-Neurociencias/neurodiagnoses/blob/main/docs/collaboration.md]]
	106	+* EBRAINS Wiki: Collabs/neurodiagnoses/Collaborations
114	114
115		-✔ **Neuroimaging Preprocessing**: MRI, PET, EEG data is preprocessed using **Clinica.Run pipelines.**
116		-✔ **Automated Biomarker Extraction**: Extracts volumetric, metabolic, and functional biomarkers.
117		-✔ **Data Security & Compliance**: Clinica.Run is **GDPR & HIPAA-compliant.**
	108	+=== **Partnering with Data Providers** ===
118	118
119		-=== **Implementation Steps** ===
	110	+Beyond using existing datasets, Neurodiagnoses seeks partnerships with data repositories to:
120	120
121		-1. Install **Clinica.Run** dependencies.
122		-1. Configure **Clinica.Run pipeline** in clinica_run_config.json.
123		-1. Run **biomarker extraction pipelines** for AI-based diagnostics.
	112	+* Enable direct API-based data integration for real-time processing.
	113	+* Co-develop harmonized AI-ready datasets with standardized annotations.
	114	+* Secure funding opportunities through joint grant applications.
124	124
125		-**Reference:** [[Clinica.Run Documentation>>url:https://github.com/Fundacion-de-Neurociencias/neurodiagnoses/blob/main/docs/clinica_run.md]]
	116	+=== **Interested in Partnering?** ===
126	126
127		-----
	118	+If you represent a research consortium or database provider, reach out to explore data-sharing agreements.
128	128
129		-== **Collaborative Development & Research** ==
	120	+* Contact: [[info@neurodiagnoses.com>>mailto:info@neurodiagnoses.com]]
130	130
131		-**We Use GitHub to Develop AI Models & Store Research Data**
132		-
133		-* **GitHub Repository:** AI model training scripts.
134		-* **GitHub Issues:** Tracks ongoing research questions.
135		-* **GitHub Wiki:** Project documentation & user guides.
136		-
137		-**We Use EBRAINS for Data & Collaboration**
138		-
139		-* **EBRAINS Buckets:** Large-scale neuroimaging and biomarker storage.
140		-* **EBRAINS Jupyter Notebooks:** Cloud-based AI model execution.
141		-* **EBRAINS Wiki:** Research documentation and updates.
142		-
143		-**Join the Project Forum:** [[GitHub Discussions>>url:https://github.com/Fundacion-de-Neurociencias/neurodiagnoses/discussions]]
144		-
145	145	----
146	146
147		-**For Additional Documentation:**
	124	+== **Final Notes** ==
148	148
149		-* **GitHub Repository:** [[Neurodiagnoses AI Models>>url:https://github.com/Fundacion-de-Neurociencias/neurodiagnoses]]
150		-* **EBRAINS Wiki:** [[Neurodiagnoses Research Collaboration>>url:https://wiki.ebrains.eu/bin/view/Collabs/neurodiagnoses/]]
	126	+Neurodiagnoses continuously expands its data ecosystem to support AI-driven clinical decision-making. Researchers and institutions are encouraged to contribute new datasets and methodologies.
151	151
152		-----
	128	+For additional technical documentation:
153	153
154		-**Neurodiagnoses is Open for Contributions – Join Us Today!**
	130	+* [[GitHub Repository>>url:https://github.com/Fundacion-de-Neurociencias/neurodiagnoses]]
	131	+* [[EBRAINS Collaboration Page>>url:https://wiki.ebrains.eu/bin/view/Collabs/neurodiagnoses/]]
	132	+
	133	+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.