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1		-XWiki.petritter
	1	+XWiki.ldomide

Content

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4	4	(((
5	5	== TVB Image Processing Pipeline ==
6	6
7		-=== [[Web-GUI to configure and start processing on HPC>>https://thevirtualbrain.apps.hbp.eu/||rel="noopener noreferrer" target="_blank"]] ===
8		-
9	9	==== [[Pipeline Video Tutorial>>https://drive.google.com/file/d/1VcXf3GX3KoihF4UzJQXzuGL4XWoqj5Jr/view||rel="noopener noreferrer" target="_blank"]] ====
10	10
11		-==== [[Direct link to notebook>>https://drive.ebrains.eu/#my-libs/lib/42ac27a5-981e-4cf6-8ec5-d67b0c24bf09/notebooks||rel="noopener noreferrer" target="_blank"]] ====
	9	+==== [[Direct link to notebook>>https://drive.ebrains.eu/d/5e2fbc74575c47e88780/||rel="noopener noreferrer" target="_blank"]] ====
12	12
13	13	[[image:8677353.png||style="float:left"]]
14	14
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22	22	(((
23	23	== Quick links ==
24	24
25		-* [[TVB Pipeline Web GUI>>https://thevirtualbrain.apps.hbp.eu/]]
26	26	* [[TVB on EBRAINS (Short Version)>>https://www.youtube.com/watch?v=EETRdGskiWQ&t=2s||rel="noopener noreferrer" target="_blank"]]
27	27	* [[TVB on EBRAINS (Long Version)>>https://www.youtube.com/watch?v=VYhR9RNRIpA&t=2s||rel="noopener noreferrer" target="_blank"]]
28	28	* [[TVB on EBRAINS (Mini Videos)>>url:https://www.youtube.com/playlist?list=PLVtblERyzDeLcVv4BbW3BvmO8D-qVZxKf||rel="noopener noreferrer" target="_blank"]]
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30	30
31	31	== What can I find here? ==
32	32
33		-* a [[link>>https://thevirtualbrain.apps.hbp.eu/]] to the Web App for using the pipeline via GUI
34	34	* the code underlying the pipeline including the orchestrator that manages processing on the supercomputer
35	35	* an IPython notebook that describes how to
36	36	** use the TVB processing pipeline on one of the associated supercomputers using PyUnicore
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51	51	== How do I use it? ==
52	52
53	53	* the pipeline is implemented by three Docker containers (mrtrix3_connectome, fmriprep and tvb_converter)
54		-* the containers are executed on supercomputers and operated via the [[web GUI>>https://thevirtualbrain.apps.hbp.eu/]] or via IPython notebooks
	50	+* the containers can be executed on supercomputers and operated via IPython notebooks
55	55	* Find the notebook by clicking on "Drive" in the left menu. The notebook is located in the folder "notebooks"
56		-* Direct link to notebook: [[https:~~/~~/drive.ebrains.eu/#my-libs/lib/42ac27a5-981e-4cf6-8ec5-d67b0c24bf09/notebooks>>url:https://drive.ebrains.eu/#my-libs/lib/42ac27a5-981e-4cf6-8ec5-d67b0c24bf09/notebooks]]
	52	+* Direct link to notebook: [[https:~~/~~/drive.ebrains.eu/d/5e2fbc74575c47e88780/>>https://drive.ebrains.eu/d/5e2fbc74575c47e88780/]]
57	57	* To use the notebook, download it onto your local filesystem, create a new Collab and upload it there.
58	58	* Then, head over to [[https:~~/~~/lab.ebrains.eu/>>url:https://lab.ebrains.eu/||rel="noopener noreferrer" target="_blank"]] to edit and run your notebook.
59	59	* Depending on whether you created a public or a private notebook it will be accessible in either "drive/Shared with all" or "drive/Shared with groups'"