Changes for page TVB PIPELINE

Last modified by ldomide on 2024/05/20 08:56
From version 7.1
edited by michaels
on 2020/05/06 09:11
Change comment: There is no comment for this version
To version 12.1
edited by michaels
on 2020/05/06 13:31
Change comment: There is no comment for this version

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5 5  = From MRI to Functional and Structural Connectivity =
6 6  
7 7  Neuroimaging data preprocessing pipeline
8 +
9 +(% style="text-align:center" %)
10 +[[image:8d975cf4-13ec-4a6d-9fd9-064bd1fac7b0.jpeg]]
11 +
12 +
8 8  )))
9 9  )))
10 10  
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12 12  (((
13 13  (% class="col-xs-12 col-sm-8" %)
14 14  (((
15 -= What can I find here? =
20 +== What can I find here? ==
16 16  
17 17  * an IPython notebook that describes how to
18 18  ** use the TVB pipeline on one of the associated supercomputers using PyUnicore
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19 19  ** upload model data to the supercomputer
20 20  ** set up and run the pipeline
21 21  ** download processing results
27 +
28 +== How do I use it? ==
29 +
30 +* the pipeline is implemented by three Docker containers (mrtrix3_connectome, fmriprep and tvb_converter)
31 +* the containers are executed on supercomputers and operated via IPython notebooks
32 +* Find the notebook by clicking on "Drive" in the left menu. The notebook is located in the folder "notebooks"
33 +* 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]]
34 +* To use the notebook, download it onto your local filesystem, create a new Collab and upload it there.
35 +* Then, head over to [[https:~~/~~/lab.ebrains.eu/>>url:https://lab.ebrains.eu/||rel="noopener noreferrer" target="_blank"]] to edit and run your notebook.
36 +* 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'"
22 22  )))
23 23  
24 24  
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1 +XWiki.michaels
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TVB PIPELINE