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1 **# Neurodiagnoses AI: Multimodal AI for Neurodiagnostic Predictions**
2
3 ## **Project Overview**
4 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**.##
5
6 ## **How to Use External Databases in Neurodiagnoses**
7 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.##
8
9 ### **Potential Data Sources**
10 Neurodiagnoses maintains an updated list of potential biomedical databases relevant to neurodegenerative diseases. ##
11
12 **Reference: List of Potential Databases**
13 - **ADNI**: Alzheimer's Disease data ([ADNI](https://adni.loni.usc.edu))
14 - **PPMI**: Parkinson’s Disease Imaging and biospecimens ([PPMI](https://www.ppmi-info.org))
15 - **GP2**: Whole-genome sequencing for PD ([GP2](https://gp2.org))
16 - **Enroll-HD**: Huntington’s Disease Clinical and genetic data ([Enroll-HD](https://www.enroll-hd.org))
17 - **GAAIN**: Multi-source Alzheimer’s data aggregation ([GAAIN](https://gaain.org))
18 - **UK Biobank**: Population-wide genetic, imaging, and health records ([UK Biobank](https://www.ukbiobank.ac.uk))
19 - **DPUK**: Dementia and Aging data ([DPUK](https://www.dementiasplatform.uk))
20 - **PRION Registry**: Prion Diseases clinical and genetic data ([PRION Registry](https://prionregistry.org))
21 - **DECIPHER**: Rare genetic disorder genomic variants ([DECIPHER](https://decipher.sanger.ac.uk))
22
23 ### **1. Register for Access**
24 - Each external database requires **individual registration** and access approval.
25 - Ensure compliance with **ethical approvals** and **data usage agreements** before integrating datasets into Neurodiagnoses.
26 - Some repositories may require a **Data Usage Agreement (DUA)** for sensitive medical data.##
27
28 ### **2. Download & Prepare Data**
29 - Download datasets while adhering to database usage policies.
30 - Ensure files meet **Neurodiagnoses format requirements**:
31 - **Tabular Data**: `.csv`, `.tsv`
32 - **Neuroimaging Data**: `.nii`, `.dcm`
33 - **Genomic Data**: `.fasta`, `.vcf`
34 - **Clinical Metadata**: `.json`, `.xml`##
35
36 - **Mandatory Fields for Integration**:
37 - **Subject ID**: Unique patient identifier
38 - **Diagnosis**: Standardized disease classification
39 - **Biomarkers**: CSF, plasma, or imaging biomarkers
40 - **Genetic Data**: Whole-genome or exome sequencing
41 - **Neuroimaging Metadata**: MRI/PET acquisition parameters
42
43 ### **3. Upload Data to Neurodiagnoses**
44 **Option 1: Upload to EBRAINS Bucket**
45 - Location: **EBRAINS Neurodiagnoses Bucket**
46 - Ensure correct **metadata tagging** before submission.##
47
48 **Option 2: Contribute via GitHub Repository**
49 - Location: **GitHub Data Repository**
50 - Create a new folder under `/data/` and include a **dataset description**.
51 - For large datasets, contact project administrators before uploading.
52
53 ### **4. Integrate Data into AI Models**
54 - Open **Jupyter Notebooks** on EBRAINS to run **preprocessing scripts**.
55 - Standardize **neuroimaging and biomarker formats** using harmonization tools.
56 - Use **machine learning models** to handle missing data and feature extraction.
57 - Train AI models with **newly integrated patient cohorts**.##
58
59 **Reference**: See `docs/data_processing.md` for detailed instructions.
60
61 ## **Collaboration & Partnerships**##
62 # **Partnering with Data Providers**
63 Neurodiagnoses seeks partnerships with data repositories to:
64 - Enable **API-based data integration** for real-time processing.
65 - Co-develop **harmonized AI-ready datasets** with standardized annotations.
66 - Secure **funding opportunities** through joint grant applications.
67
68 **Interested in Partnering?**
69 - If you represent a research consortium or database provider, reach out to explore data-sharing agreements.
70 - **Contact**: info@neurodiagnoses.com
71
72 ## **Final Notes**
73 Neurodiagnoses continuously expands its data ecosystem to support AI-driven clinical decision-making. Researchers and institutions are encouraged to contribute **new datasets and methodologies**.##
74
75 For additional technical documentation:
76 - **GitHub Repository**: [Neurodiagnoses GitHub](https://github.com/neurodiagnoses)
77 - **EBRAINS Collaboration Page**: [EBRAINS Neurodiagnoses](https://ebrains.eu/collabs/neurodiagnoses)
78
79 If you experience issues integrating data, **open a GitHub Issue** or consult the **EBRAINS Neurodiagnoses Forum**.
80
81 == **How to Use External Databases in Neurodiagnoses** ==
82
83 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.
84
85 === **Potential Data Sources** ===
86
87 Neurodiagnoses maintains an updated list of potential biomedical databases relevant to neurodegenerative diseases.
88
89 * Reference: [[List of Potential Databases>>url:https://github.com/Fundacion-de-Neurociencias/neurodiagnoses/blob/main/data/sources/list_of_potential_databases]]
90
91 === **1. Register for Access** ===
92
93 Each external database requires individual registration and access approval. Follow the official guidelines of each database provider.
94
95 * Ensure that you have completed all ethical approvals and data access agreements before integrating datasets into Neurodiagnoses.
96 * Some repositories require a Data Usage Agreement (DUA) before downloading sensitive medical data.
97
98 === **2. Download & Prepare Data** ===
99
100 Once access is granted, download datasets while complying with data usage policies. Ensure that the files meet Neurodiagnoses’ format requirements for smooth integration.
101
102 ==== **Supported File Formats** ====
103
104 * Tabular Data: .csv, .tsv
105 * Neuroimaging Data: .nii, .dcm
106 * Genomic Data: .fasta, .vcf
107 * Clinical Metadata: .json, .xml
108
109 ==== **Mandatory Fields for Integration** ====
110
111 |=Field Name|=Description
112 |Subject ID|Unique patient identifier
113 |Diagnosis|Standardized disease classification
114 |Biomarkers|CSF, plasma, or imaging biomarkers
115 |Genetic Data|Whole-genome or exome sequencing
116 |Neuroimaging Metadata|MRI/PET acquisition parameters
117
118 === **3. Upload Data to Neurodiagnoses** ===
119
120 Once preprocessed, data can be uploaded to EBRAINS or GitHub.
121
122 * (((
123 **Option 1: Upload to EBRAINS Bucket**
124
125 * Location: [[EBRAINS Neurodiagnoses Bucket>>url:https://wiki.ebrains.eu/bin/view/Collabs/neurodiagnoses/Bucket]]
126 * Ensure correct metadata tagging before submission.
127 )))
128 * (((
129 **Option 2: Contribute via GitHub Repository**
130
131 * Location: [[GitHub Data Repository>>url:https://github.com/Fundacion-de-Neurociencias/neurodiagnoses/tree/main/data]]
132 * Create a new folder under /data/ and include dataset description.
133 )))
134
135 //Note: For large datasets, please contact the project administrators before uploading.//
136
137 === **4. Integrate Data into AI Models** ===
138
139 Once uploaded, datasets must be harmonized and formatted before AI model training.
140
141 ==== **Steps for Data Integration** ====
142
143 * Open Jupyter Notebooks on EBRAINS to run preprocessing scripts.
144 * Standardize neuroimaging and biomarker formats using harmonization tools.
145 * Use machine learning models to handle missing data and feature extraction.
146 * Train AI models with newly integrated patient cohorts.
147 * 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]].
148
149 ----
150
151 == **Database Sources Table** ==
152
153 === **Where to Insert This** ===
154
155 * GitHub: [[docs/data_sources.md>>url:https://github.com/Fundacion-de-Neurociencias/neurodiagnoses/blob/main/docs/data_sources.md]]
156 * EBRAINS Wiki: Collabs/neurodiagnoses/Data Sources
157
158 === **Key Databases for Neurodiagnoses** ===
159
160 |=Database|=Focus Area|=Data Type|=Access Link
161 |ADNI|Alzheimer's Disease|MRI, PET, CSF, cognitive tests|ADNI
162 |PPMI|Parkinson’s Disease|Imaging, biospecimens|[[PPMI>>url:https://www.ppmi-info.org/]]
163 |GP2|Genetic Data for PD|Whole-genome sequencing|[[GP2>>url:https://gp2.org/]]
164 |Enroll-HD|Huntington’s Disease|Clinical, genetic, imaging|[[Enroll-HD>>url:https://enroll-hd.org/]]
165 |GAAIN|Alzheimer's & Cognitive Decline|Multi-source data aggregation|[[GAAIN>>url:https://www.gaain.org/]]
166 |UK Biobank|Population-wide studies|Genetic, imaging, health records|[[UK Biobank>>url:https://www.ukbiobank.ac.uk/]]
167 |DPUK|Dementia & Aging|Imaging, genetics, lifestyle factors|[[DPUK>>url:https://www.dementiasplatform.uk/]]
168 |PRION Registry|Prion Diseases|Clinical and genetic data|[[PRION Registry>>url:https://www.prionalliance.org/]]
169 |DECIPHER|Rare Genetic Disorders|Genomic variants|DECIPHER
170
171 If you know a relevant dataset, submit a proposal in [[GitHub Issues>>url:https://github.com/Fundacion-de-Neurociencias/neurodiagnoses/issues]].
172
173 ----
174
175 == **Collaboration & Partnerships** ==
176
177 === **Where to Insert This** ===
178
179 * GitHub: [[docs/collaboration.md>>url:https://github.com/Fundacion-de-Neurociencias/neurodiagnoses/blob/main/docs/collaboration.md]]
180 * EBRAINS Wiki: Collabs/neurodiagnoses/Collaborations
181
182 === **Partnering with Data Providers** ===
183
184 Beyond using existing datasets, Neurodiagnoses seeks partnerships with data repositories to:
185
186 * Enable direct API-based data integration for real-time processing.
187 * Co-develop harmonized AI-ready datasets with standardized annotations.
188 * Secure funding opportunities through joint grant applications.
189
190 === **Interested in Partnering?** ===
191
192 If you represent a research consortium or database provider, reach out to explore data-sharing agreements.
193
194 * Contact: [[info@neurodiagnoses.com>>mailto:info@neurodiagnoses.com]]
195
196 ----
197
198 == **Final Notes** ==
199
200 Neurodiagnoses continuously expands its data ecosystem to support AI-driven clinical decision-making. Researchers and institutions are encouraged to contribute new datasets and methodologies.
201
202 For additional technical documentation:
203
204 * [[GitHub Repository>>url:https://github.com/Fundacion-de-Neurociencias/neurodiagnoses]]
205 * [[EBRAINS Collaboration Page>>url:https://wiki.ebrains.eu/bin/view/Collabs/neurodiagnoses/]]
206
207 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.