Changes for page TVB PIPELINE

Last modified by ldomide on 2024/05/20 08:56
From version 36.1
edited by michaels
on 2020/08/03 11:11
Change comment: There is no comment for this version
To version 41.1
edited by michaels
on 2021/11/30 10:58
Change comment: There is no comment for this version

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2 2  (((
3 3  (% class="container" %)
4 4  (((
5 -= TVB Image Processing Pipeline With MINDS annotated Outputs =
5 +== TVB Image Processing Pipeline ==
6 6  
7 -== [[Pipeline Video Tutorial>>https://drive.google.com/file/d/1VcXf3GX3KoihF4UzJQXzuGL4XWoqj5Jr/view||rel="noopener noreferrer" target="_blank"]] ==
7 +=== [[Web-GUI to configure and start processing on HPC>>https://thevirtualbrain.apps.hbp.eu/||rel="noopener noreferrer" target="_blank"]] ===
8 8  
9 -== [[Direct link to notebook>>https://drive.ebrains.eu/#my-libs/lib/42ac27a5-981e-4cf6-8ec5-d67b0c24bf09/notebooks||rel="noopener noreferrer" target="_blank"]] ==
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"]] ====
12 +
11 11  [[image:8677353.png||style="float:left"]]
12 12  
13 13  
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20 20  (((
21 21  == Quick links ==
22 22  
23 -* [[TVB on EBRAINS (Short Version)>>https://www.youtube.com/watch?v=EETRdGskiWQ&t=2s||rel=" noopener noreferrer" target="_blank"]]
24 -* [[TVB on EBRAINS (Long Version)>>https://www.youtube.com/watch?v=VYhR9RNRIpA&t=2s||rel=" noopener noreferrer" target="_blank"]]
25 -* [[TVB on EBRAINS (Mini Videos)>>url:https://www.youtube.com/playlist?list=PLVtblERyzDeLcVv4BbW3BvmO8D-qVZxKf||rel=" noopener noreferrer" target="_blank"]]
25 +* [[TVB Pipeline Web GUI>>https://thevirtualbrain.apps.hbp.eu/]]
26 +* [[TVB on EBRAINS (Short Version)>>https://www.youtube.com/watch?v=EETRdGskiWQ&t=2s||rel="noopener noreferrer" target="_blank"]]
27 +* [[TVB on EBRAINS (Long Version)>>https://www.youtube.com/watch?v=VYhR9RNRIpA&t=2s||rel="noopener noreferrer" target="_blank"]]
28 +* [[TVB on EBRAINS (Mini Videos)>>url:https://www.youtube.com/playlist?list=PLVtblERyzDeLcVv4BbW3BvmO8D-qVZxKf||rel="noopener noreferrer" target="_blank"]]
26 26  * [[User Story>>url:https://wiki.ebrains.eu/bin/view/Collabs/user-story-tvb/]]
27 27  
28 28  == What can I find here? ==
29 29  
33 +* a [[link>>https://thevirtualbrain.apps.hbp.eu/]] to the Web App for using the pipeline via GUI
34 +* the code underlying the pipeline including the orchestrator that manages processing on the supercomputer
30 30  * an IPython notebook that describes how to
31 31  ** use the TVB processing pipeline on one of the associated supercomputers using PyUnicore
32 32  ** upload MRI data to the supercomputer
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46 46  == How do I use it? ==
47 47  
48 48  * the pipeline is implemented by three Docker containers (mrtrix3_connectome, fmriprep and tvb_converter)
49 -* the containers are executed on supercomputers and operated via IPython notebooks
54 +* the containers are executed on supercomputers and operated via the [[web GUI>>https://thevirtualbrain.apps.hbp.eu/]] or via IPython notebooks
50 50  * Find the notebook by clicking on "Drive" in the left menu. The notebook is located in the folder "notebooks"
51 51  * 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 52  * To use the notebook, download it onto your local filesystem, create a new Collab and upload it there.
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TVB PIPELINE