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1		-~== Neurodiagnoses: AI-Powered Diagnosis ==
	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.
2	2
3		-Neurodiagnoses provides ~*~*two AI-assisted diagnostic systems~*~*, allowing clinicians to compare a ~*~*probabilistic~*~* and a ~*~*structured tridimensional approach~*~*.
	5	+~-~--
4	4
	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	+
5	5	~-~--
6	6
7		-~===  Available Notebooks ===
8		-Below are the Jupyter Notebooks implementing these diagnostic methods:
	27	+~=== How to Run Notebooks ===
	28	+To use the notebooks, follow these steps:
9	9
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.
	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.
20	20
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.
	36	+~-~--
28	28
29		-Both notebooks run on ~*~*EBRAINS Jupyter Lab~*~* and are available for real-time clinical testing.
	38	+~=== Contribute a New Notebook ===
	39	+Do you have a notebook to contribute? Follow these steps:
30	30
	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	+
31	31	~-~--
	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/)
32	32