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Author

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1		-XWiki.fousekjan
	1	+XWiki.gorkazl

Content

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24	24	(((
25	25	Running the notebooks //**requires an EBRANS account**// with permissions to access the Lab and programmatic access to the Knowledge Graph API. In addition, to interact with the HPC infrastructure, the user needs access to an active allocation on the corresponding FENIX site. Lastly, the virtual ageing brain notebooks write data to the Bucket storage.
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27		-Please, to avoid overwriting precomputed data, //**make first a private working duplicate**// of this Collab using the notebook [[copy_showcase1_collab.ipynb>>https://lab.ch.ebrains.eu/hub/user-redirect/lab/tree/shared/SGA3%20D1.2%20Showcase%201/copy_showcase1_collab.ipynb]]. If you encounter any issues running the notebooks, contact [[The Virtual Brain Facility Hub>>mailto:jan.fousek@univ-amu.fr]].
	27	+Please, to be able to interact with the material fully, //**make first a private working duplicate**// of this Collab using the notebook [[copy_showcase1_collab.ipynb>>https://lab.ch.ebrains.eu/hub/user-redirect/lab/tree/shared/SGA3%20D1.5%20Showcase%201/copy_showcase1_collab.ipynb]]. If you encounter any issues running the notebooks, contact [[The Virtual Brain Facility Hub>>mailto:jan.fousek@univ-amu.fr]].
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29	29	)))
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36	36	(% class="wikigeneratedid" %)
37	37	See the details of the first study in the following publication:
38	38
39		-M. Lavanga, J. Stumme, B. H. Yalcinkaya, J. Fousek, C. Jockwitz, H. Sheheitli, N. Bittner, M. Hashemi, S. Petkoski, S. Caspers, and V. Jirsa, [[The Virtual Aging Brain: A Model-Driven Explanation for Cognitive Decline in Older Subjects>>https://doi.org/10.1101/2022.02.17.480902]].
	39	+Lavanga, M., Stumme, J., Yalcinkaya, B. H., Fousek, J., Jockwitz, C., Sheheitli, H., Bittner, N., Hashemi, M., Petkoski, S., Caspers, S., & Jirsa, V. (2023)[[. The virtual aging brain: Causal inference supports interhemispheric dedifferentiation in healthy aging.>>https://doi.org/10.1016/j.neuroimage.2023.120403]] //NeuroImage//, //283//, 120403.
40	40
41	41	=== Simulation of resting-state activity ===
42	42
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49	49
50	50	Link to the notebook:
51	51
52		-* [[virtual_ageing/notebooks/1_BNM_for_resting_state.ipynb>>https://lab.ch.ebrains.eu/user-redirect/lab/tree/shared/SGA3%20D1.2%20Showcase%201/virtual_ageing/notebooks/1_BNM_for_resting_state.ipynb]]
	52	+* [[virtual_ageing/notebooks/1_BNM_for_resting_state.ipynb>>https://lab.ch.ebrains.eu/hub/user-redirect/lab/tree/shared/SGA3%20D1.5%20Showcase%201/virtual_ageing/notebooks/1_BNM_for_resting_state.ipynb]]
53	53
54		-
55	55	[[image:https://wiki.ebrains.eu/bin/download/Collabs/sga3-d1-2-showcase-1/WebHome/image-20220103100841-2.png?rev=1.1||alt="image-20220103100841-2.png"]]
56	56
57	57	=== Virtual ageing trajectories ===
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64	64
65	65	Link to the notebook:
66	66
67		-* [[virtual_ageing/notebooks/2_virtual_ageing_trajectories.ipynb>>https://lab.ch.ebrains.eu/user-redirect/lab/tree/shared/SGA3%20D1.2%20Showcase%201/virtual_ageing/notebooks/2_virtual_ageing_trajectories.ipynb]]
	66	+* [[virtual_ageing/notebooks/2_virtual_ageing_trajectories.ipynb>>https://lab.ch.ebrains.eu/hub/user-redirect/lab/tree/shared/SGA3%20D1.5%20Showcase%201/virtual_ageing/notebooks/2_virtual_ageing_trajectories.ipynb]]
68	68
69	69	[[image:https://wiki.ebrains.eu/bin/download/Collabs/sga3-d1-2-showcase-1/WebHome/image-20220103101022-3.png?rev=1.1||alt="image-20220103101022-3.png"]]
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76	76
77	77	Link to the notebook:
78	78
79		-* [[virtual_ageing/notebooks/3_inference_with_SBI.ipynb>>https://lab.ch.ebrains.eu/user-redirect/lab/tree/shared/SGA3%20D1.2%20Showcase%201/virtual_ageing/notebooks/3_inference_with_SBI.ipynb]]
	78	+* [[virtual_ageing/notebooks/3_inference_with_SBI.ipynb>>https://lab.ch.ebrains.eu/hub/user-redirect/lab/tree/shared/SGA3%20D1.5%20Showcase%201/virtual_ageing/notebooks/3_inference_with_SBI.ipynb]]
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	80	+== ==
	81	+
81	81	== b. Regional variability – Receptor density maps ==
82	82
83	83	Aims at demonstrating the construction of whole-brain network models of the brain's activity, accounting for differences in receptor densities across cortical regions.
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92	92
93	93	The three datasets are characterised in the same parcellation. Link to the notebook:
94	94
95		-* [[regional_variability/notebooks/1_load_data.ipynb>>https://lab.ch.ebrains.eu/hub/user-redirect/lab/tree/shared/SGA3%20D1.2%20Showcase%201/regional_variability/notebooks/1_load_data.ipynb]]
	96	+* [[regional_variability/1_load_fMRI_data.ipynb>>https://lab.ch.ebrains.eu/hub/user-redirect/lab/tree/shared/SGA3%20D1.5%20Showcase%201/regional_variability/1_load_fMRI_data.ipynb]]
	97	+* [[regional_variability/2_retrieve_receptor_maps.ipynb>>https://lab.ch.ebrains.eu/hub/user-redirect/lab/tree/shared/SGA3%20D1.5%20Showcase%201/regional_variability/2_retrieve_receptor_maps.ipynb]]
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97	97	[[image:https://wiki.ebrains.eu/bin/download/Collabs/sga3-d1-2-showcase-1/WebHome/download%20-%202022-02-10T130815.902.png?rev=1.1||alt="region-wise gene expression heterogeneity"]]
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102	102
103	103	Link to the notebook:
104	104
105		-* [[regional_variability/notebooks/2_parameter_swep.ipynb>>https://lab.ch.ebrains.eu/hub/user-redirect/lab/tree/shared/SGA3%20D1.2%20Showcase%201/regional_variability/notebooks/2_parameter_swep.ipynb]]
	107	+* [[regional_variability/notebooks/2_parameter_swep.ipynb>>https://lab.ch.ebrains.eu/hub/user-redirect/lab/tree/shared/SGA3%20D1.5%20Showcase%201/regional_variability/notebooks/2_parameter_swep.ipynb]]
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107	107	[[image:https://wiki.ebrains.eu/bin/download/Collabs/sga3-d1-2-showcase-1/WebHome/download%20-%202022-02-10T131102.033.png?rev=1.1||alt="regional bias vs goodness of fit"]]
108	108	)))