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1		-~== Neurodiagnoses: Jupyter Notebooks ==
2		-Welcome to the Jupyter Notebooks Hub for the Neurodiagnoses project.
3		-Here, you will find a collection of AI-powered notebooks used for processing biomarkers, training AI models, and performing neuroimaging analysis.
	1	+~== Neurodiagnoses: AI-Powered Diagnosis ==
4	4
5		-~-~--
	3	+Neurodiagnoses provides ~*~*two AI-assisted diagnostic systems~*~*, allowing clinicians to compare a ~*~*probabilistic~*~* and a ~*~*structured tridimensional approach~*~*.
6	6
7		-~=== Available Notebooks ===
8		-Below is a list of Jupyter Notebooks available in EBRAINS. Click on any notebook to open it.
9		-
10		-~1. ~*~*Biomarker Classifier~*~*
11		- Link: [Open Notebook](https:~/~/lab.jsc.ebrains.eu/hub/user-redirect/lab/tree/shared/Neurodiagnoses/biomarker_classifier.ipynb)
12		- Description: Trains a machine learning model to classify patients based on biomarkers (Amyloid-beta, Tau, NFL).
13		- Usage: Run all cells to train the model and generate predictions.
14		-
15		-2. ~*~*MRI Feature Extraction~*~* (Coming Soon)
16		- Link: Notebook Link TBD
17		- Description: Uses AI to extract neuroanatomical features from MRI scans.
18		- Usage: Upload MRI data and run the script to generate reports.
19		-
20		-3. ~*~*EEG Analysis with Deep Learning~*~* (Coming Soon)
21		- Link: Notebook Link TBD
22		- Description: Uses deep learning models to analyze EEG patterns and detect abnormalities.
23		- Usage: Load EEG recordings and apply pre-trained AI models.
24		-
25	25	~-~--
26	26
27		-~=== How to Run Notebooks ===
28		-To use the notebooks, follow these steps:
	7	+~===  Available Notebooks ===
	8	+Below are the Jupyter Notebooks implementing these diagnostic methods:
29	29
30		-~1. Click on a notebook link above to open it inside EBRAINS Jupyter Lab.
31		-2. If prompted, select the Python 3 (ipykernel) kernel.
32		-3. Run each cell sequentially (Shift + Enter).
33		-4. Check outputs and modify parameters as needed.
34		-5. Download results if necessary.
	10	+~1. ~*~*Probabilistic Diagnosis Notebook~*~*
	11	+ - [Open Notebook](https:~/~/lab.jsc.ebrains.eu/hub/user-redirect/lab/tree/shared/Neurodiagnoses/probabilistic_diagnosis.ipynb)
	12	+ - AI assigns multiple possible diagnoses with probability percentages.
	13	+ - Example:
	14	+ ```
	15	+ 70% Frontotemporal Dementia
	16	+ 25% Vascular Dementia
	17	+ 5% Normal Pressure Hydrocephalus
	18	+ ```
	19	+ - ~*~*Use Case:~*~* Ranking differential diagnoses in complex cases.
35	35
36		-~-~--
	21	+2. ~*~*Tridimensional Diagnosis Notebook~*~*
	22	+ - [Open Notebook](https:~/~/lab.jsc.ebrains.eu/hub/user-redirect/lab/tree/shared/Neurodiagnoses/tridimensional_diagnosis.ipynb)
	23	+ - AI provides structured diagnostic annotations based on:
	24	+ - Axis 1: ~*~*Etiology~*~* (genetic, metabolic, autoimmune, vascular)
	25	+ - Axis 2: ~*~*Molecular Biomarkers~*~* (CSF, PET, EEG, MRI features)
	26	+ - Axis 3: ~*~*Neuroanatomoclinical Correlations~*~* (functional brain regions, atrophy)
	27	+ - ~*~*Use Case:~*~* Precision neurology for biomarker-based classification.
37	37
38		-~=== Contribute a New Notebook ===
39		-Do you have a notebook to contribute? Follow these steps:
	29	+Both notebooks run on ~*~*EBRAINS Jupyter Lab~*~* and are available for real-time clinical testing.
40	40
41		-~1. Create a new Jupyter Notebook in EBRAINS.
42		-2. Save it inside `/shared/Neurodiagnoses/`.
43		-3. Add the notebook link to this page.
44		-4. Ensure documentation is included in the first cell.
45		-
46	46	~-~--
47		-
48		-~=== Additional Resources ===
49		-- EBRAINS Jupyter Lab: [Visit Here](https:~/~/lab.jsc.ebrains.eu/)
50		-- GitHub Repository: [Neurodiagnoses GitHub](https:~/~/github.com/manuelmenendezgonzalez/neurodiagnoses)
51		-- Project Wiki: [Neurodiagnoses Wiki](https:~/~/wiki.ebrains.eu/bin/view/Collabs/neurodiagnoses/)
52	52