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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. The methodology integrates multi-modal data, including genetic, neuroimaging, neurophysiological, and biomarker datasets, and applies machine learning models to generate structured, explainable diagnostic outputs.
	3	+Neurodiagnoses develops a **tridimensional diagnostic framework** for **CNS diseases**, incorporating **AI-powered annotation tools** to improve **interpretability, standardization, and clinical utility.**
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	+
5	5	----
6	6
7		-== **How to Use External Databases in Neurodiagnoses** ==
	15	+== **Data Integration & External Databases** ==
8	8
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.
	17	+=== **How to Use External Databases in Neurodiagnoses** ===
10	10
11		-=== **Potential Data Sources** ===
	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.
12	12
13		-Neurodiagnoses maintains an updated list of potential biomedical databases relevant to neurodegenerative diseases.
	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]]
14	14
15		-* Reference: [[List of Potential Databases>>url:https://github.com/Fundacion-de-Neurociencias/neurodiagnoses/blob/main/data/sources/list_of_potential_databases]]
	24	+=== **Register for Access** ===
16	16
17		-=== **1. Register for Access** ===
	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).**
18	18
19		-Each external database requires individual registration and access approval. Follow the official guidelines of each database provider.
	30	+=== **Download & Prepare Data** ===
20	20
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.
	32	+Once access is granted, download datasets **following compliance guidelines** and **format requirements** for integration.
23	23
24		-=== **2. Download & Prepare Data** ===
	34	+**Supported File Formats**
25	25
26		-Once access is granted, download datasets while complying with data usage policies. Ensure that the files meet Neurodiagnoses’ format requirements for smooth integration.
	36	+* **Tabular Data**: .csv, .tsv
	37	+* **Neuroimaging Data**: .nii, .dcm
	38	+* **Genomic Data**: .fasta, .vcf
	39	+* **Clinical Metadata**: .json, .xml
27	27
28		-==== **Supported File Formats** ====
	41	+**Mandatory Fields for Integration**
29	29
30		-* Tabular Data: .csv, .tsv
31		-* Neuroimaging Data: .nii, .dcm
32		-* Genomic Data: .fasta, .vcf
33		-* Clinical Metadata: .json, .xml
	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
34	34
35		-==== **Mandatory Fields for Integration** ====
	50	+=== **Upload Data to Neurodiagnoses** ===
36	36
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
	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]]
43	43
44		-=== **3. Upload Data to Neurodiagnoses** ===
	55	+**For large datasets, please contact project administrators before uploading.**
45	45
46		-Once preprocessed, data can be uploaded to EBRAINS or GitHub.
	57	+=== **Integrate Data into AI Models** ===
47	47
48		-* (((
49		-**Option 1: Upload to EBRAINS Bucket**
	59	+Use **Jupyter Notebooks** on EBRAINS for **data preprocessing.**
	60	+Standardize data using **harmonization tools.**
	61	+Train AI models with **newly integrated datasets.**
50	50
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**
	63	+**Reference:** [[Data Processing Guide>>url:https://github.com/Fundacion-de-Neurociencias/neurodiagnoses/blob/main/docs/data_processing.md]]
56	56
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		-)))
	65	+----
60	60
61		-//Note: For large datasets, please contact the project administrators before uploading.//
	67	+== **AI-Powered Annotation & Machine Learning Models** ==
62	62
63		-=== **4. Integrate Data into AI Models** ===
	69	+Neurodiagnoses applies **advanced machine learning models** to classify CNS diseases, extract features from **biomarkers and neuroimaging**, and provide **AI-powered annotation.**
64	64
65		-Once uploaded, datasets must be harmonized and formatted before AI model training.
	71	+=== **AI Model Categories** ===
66	66
67		-==== **Steps for Data Integration** ====
	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
68	68
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]].
	80	+**Reference:** [[AI Model Documentation>>url:https://github.com/Fundacion-de-Neurociencias/neurodiagnoses/blob/main/docs/models.md]]
74	74
75	75	----
76	76
77		-== **Database Sources Table** ==
	84	+== **Clinical Decision Support & Tridimensional Diagnostic Framework** ==
78	78
79		-=== **Where to Insert This** ===
	86	+Neurodiagnoses generates **structured AI reports** for clinicians, combining:
80	80
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
	88	+**Probabilistic Diagnosis:** AI-generated ranking of potential diagnoses.
	89	+**Tridimensional Classification:** Standardized diagnostic reports based on:
83	83
84		-=== **Key Databases for Neurodiagnoses** ===
	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.
85	85
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
	95	+**Reference:** [[Tridimensional Classification Guide>>url:https://github.com/Fundacion-de-Neurociencias/neurodiagnoses/blob/main/docs/classification.md]]
96	96
97		-If you know a relevant dataset, submit a proposal in [[GitHub Issues>>url:https://github.com/Fundacion-de-Neurociencias/neurodiagnoses/issues]].
98		-
99	99	----
100	100
101		-== **Collaboration & Partnerships** ==
	99	+== **Data Security, Compliance & Federated Learning** ==
102	102
103		-=== **Where to Insert This** ===
	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	104
105		-* GitHub: [[docs/collaboration.md>>url:https://github.com/Fundacion-de-Neurociencias/neurodiagnoses/blob/main/docs/collaboration.md]]
106		-* EBRAINS Wiki: Collabs/neurodiagnoses/Collaborations
	105	+**Reference:** [[Data Protection & Federated Learning>>url:https://github.com/Fundacion-de-Neurociencias/neurodiagnoses/blob/main/docs/security.md]]
107	107
108		-=== **Partnering with Data Providers** ===
	107	+----
109	109
110		-Beyond using existing datasets, Neurodiagnoses seeks partnerships with data repositories to:
	109	+== **Data Processing & Integration with Clinica.Run** ==
111	111
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.
	111	+Neurodiagnoses now supports **Clinica.Run**, an **open-source neuroimaging platform** for **multimodal data processing.**
115	115
116		-=== **Interested in Partnering?** ===
	113	+=== **How It Works** ===
117	117
118		-If you represent a research consortium or database provider, reach out to explore data-sharing agreements.
	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.**
119	119
120		-* Contact: [[info@neurodiagnoses.com>>mailto:info@neurodiagnoses.com]]
	119	+=== **Implementation Steps** ===
121	121
	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.
	124	+
	125	+**Reference:** [[Clinica.Run Documentation>>url:https://github.com/Fundacion-de-Neurociencias/neurodiagnoses/blob/main/docs/clinica_run.md]]
	126	+
122	122	----
123	123
124		-== **Final Notes** ==
	129	+== **Collaborative Development & Research** ==
125	125
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.
	131	+**We Use GitHub to Develop AI Models & Store Research Data**
127	127
128		-For additional technical documentation:
	133	+* **GitHub Repository:** AI model training scripts.
	134	+* **GitHub Issues:** Tracks ongoing research questions.
	135	+* **GitHub Wiki:** Project documentation & user guides.
129	129
130		-* [[GitHub Repository>>url:https://github.com/Fundacion-de-Neurociencias/neurodiagnoses]]
131		-* [[EBRAINS Collaboration Page>>url:https://wiki.ebrains.eu/bin/view/Collabs/neurodiagnoses/]]
	137	+**We Use EBRAINS for Data & Collaboration**
132	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.
	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	+----
	146	+
	147	+**For Additional Documentation:**
	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/]]
	151	+
	152	+----
	153	+
	154	+**Neurodiagnoses is Open for Contributions – Join Us Today!**