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1		-==== **Overview** ====
	1	+== **Overview** ==
2	2
3	3	This project 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	+== **Workflow** ==
	6	+
	7	+1. (((
	8	+**We Use GitHub to [[Store and develop AI models, scripts, and annotation pipelines.>>https://github.com/Fundacion-de-Neurociencias/neurodiagnoses/discussions]]**
	9	+
	10	+* Create a **GitHub repository** for AI scripts and models.
	11	+* Use **GitHub Projects** to manage research milestones.
	12	+)))
	13	+1. (((
	14	+**We Use EBRAINS for Data & Collaboration**
	15	+
	16	+* Store **biomarker and neuroimaging data** in **EBRAINS Buckets**.
	17	+* Run **Jupyter Notebooks** in **EBRAINS Lab** to test AI models.
	18	+* Use **EBRAINS Wiki** for structured documentation and research discussion.
	19	+)))
	20	+
5	5	----
6	6
7		-=== **1. Data Integration** ===
	23	+== **1. Data Integration** ==
8	8
	25	+=== **EBRAINS Medical Informatics Platform (MIP)**. ===
	26	+
	27	+Neurodiagnoses integrates clinical data via the **EBRAINS Medical Informatics Platform (MIP)**. MIP federates decentralized clinical data, allowing Neurodiagnoses to securely access and process sensitive information for AI-based diagnostics.
	28	+
	29	+==== How It Works ====
	30	+
	31	+
	32	+1. (((
	33	+**Authentication & API Access:**
	34	+
	35	+* Users must have an **EBRAINS account**.
	36	+* Neurodiagnoses uses **secure API endpoints** to fetch clinical data (e.g., from the **Federation for Dementia**).
	37	+)))
	38	+1. (((
	39	+**Data Mapping & Harmonization:**
	40	+
	41	+* Retrieved data is **normalized** and converted to standard formats (.csv, .json).
	42	+* Data from **multiple sources** is harmonized to ensure consistency for AI processing.
	43	+)))
	44	+1. (((
	45	+**Security & Compliance:**
	46	+
	47	+* All data access is **logged and monitored**.
	48	+* Data remains on **MIP servers** using **federated learning techniques** when possible.
	49	+* Access is granted only after signing a **Data Usage Agreement (DUA)**.
	50	+)))
	51	+
	52	+==== Implementation Steps ====
	53	+
	54	+
	55	+1. Clone the repository.
	56	+1. Configure your **EBRAINS API credentials** in mip_integration.py.
	57	+1. Run the script to **download and harmonize clinical data**.
	58	+1. Process the data for **AI model training**.
	59	+
	60	+For more detailed instructions, please refer to the **[[MIP Documentation>>url:https://mip.ebrains.eu/]]**.
	61	+
	62	+----
	63	+
	64	+=== Data Processing & Integration with Clinica.Run ===
	65	+
	66	+Neurodiagnoses now supports **Clinica.Run**, an open-source neuroimaging platform designed for **multimodal data processing and reproducible neuroscience workflows**.
	67	+
	68	+==== How It Works ====
	69	+
	70	+
	71	+1. (((
	72	+**Neuroimaging Preprocessing:**
	73	+
	74	+* MRI, PET, EEG data is preprocessed using **Clinica.Run pipelines**.
	75	+* Supports **longitudinal and cross-sectional analyses**.
	76	+)))
	77	+1. (((
	78	+**Automated Biomarker Extraction:**
	79	+
	80	+* Standardized extraction of **volumetric, metabolic, and functional biomarkers**.
	81	+* Integration with machine learning models in Neurodiagnoses.
	82	+)))
	83	+1. (((
	84	+**Data Security & Compliance:**
	85	+
	86	+* Clinica.Run operates in **compliance with GDPR and HIPAA**.
	87	+* Neuroimaging data remains **within the original storage environment**.
	88	+)))
	89	+
	90	+==== Implementation Steps ====
	91	+
	92	+
	93	+1. Install **Clinica.Run** dependencies.
	94	+1. Configure your **Clinica.Run pipeline** in clinica_run_config.json.
	95	+1. Run the pipeline for **preprocessing and biomarker extraction**.
	96	+1. Use processed neuroimaging data for **AI-driven diagnostics** in Neurodiagnoses.
	97	+
	98	+For further information, refer to **[[Clinica.Run Documentation>>url:https://clinica.run/]]**.
	99	+
	100	+==== ====
	101	+
9	9	==== **Data Sources** ====
10	10
	104	+[[List of potential sources of databases>>https://github.com/Fundacion-de-Neurociencias/neurodiagnoses/blob/main/data/sources/list_of_potential_databases]]
	105	+
11	11	**Biomedical Ontologies & Databases:**
12	12
13	13	* **Human Phenotype Ontology (HPO)** for symptom annotation.
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16	16	**Dimensionality Reduction and Interpretability:**
17	17
18	18	* **Evaluate interpretability** using metrics like the **Area Under the Interpretability Curve (AUIC)**.
19		-* **Leverage DEIBO (Data-driven Embedding Interpretation Based on Ontologies)** to connect model dimensions to ontology concepts.
	114	+* **Leverage [[DEIBO>>https://github.com/Mellandd/DEIBO]] (Data-driven Embedding Interpretation Based on Ontologies)** to connect model dimensions to ontology concepts.
20	20
21	21	**Neuroimaging & EEG/MEG Data:**
22	22
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44	44
45	45	----
46	46
47		-=== **2. AI-Based Analysis** ===
	142	+== **2. AI-Based Analysis** ==
48	48
49	49	==== **Machine Learning & Deep Learning Models** ====
50	50
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68	68
69	69	----
70	70
71		-=== **3. Diagnostic Framework & Clinical Decision Support** ===
	166	+== **3. Diagnostic Framework & Clinical Decision Support** ==
72	72
73	73	==== **Tridimensional Diagnostic Axes** ====
74	74
...	...	@@ -89,7 +89,7 @@
89	89
90	90	----
91	91
92		-=== **4. Computational Workflow & Annotation Pipelines** ===
	187	+== **4. Computational Workflow & Annotation Pipelines** ==
93	93
94	94	==== **Data Processing Steps** ====
95	95
...	...	@@ -114,7 +114,7 @@
114	114
115	115	----
116	116
117		-=== **5. Validation & Real-World Testing** ===
	212	+== **5. Validation & Real-World Testing** ==
118	118
119	119	==== **Prospective Clinical Study** ====
120	120
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129	129
130	130	----
131	131
132		-=== **6. Collaborative Development** ===
	227	+== **6. Collaborative Development** ==
133	133
134	134	The project is **open to contributions** from **researchers, clinicians, and developers**.
135	135
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144	144
145	145	----
146	146
147		-=== **7. Tools and Technologies** ===
	242	+== **7. Tools and Technologies** ==
148	148
149	149	==== **Programming Languages:** ====
150	150
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168	168
169	169	=== **Why This Matters** ===
170	170
171		-* **The annotation system ensures that AI-generated insights are structured, interpretable, and clinically meaningful.**
172		-* **It enables real-time tracking of disease progression across the three diagnostic axes.**
173		-* **It facilitates integration with electronic health records and decision-support tools, improving AI adoption in clinical workflows.**
	266	+* The annotation system ensures that AI-generated insights are structured, interpretable, and clinically meaningful.
	267	+* It enables real-time tracking of disease progression across the three diagnostic axes.
	268	+* It facilitates integration with electronic health records and decision-support tools, improving AI adoption in clinical workflows.