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 19.1
edited by michaels
on 2020/05/06 14:08
Change comment: There is no comment for this version

Summary

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1 +tool|CHARITE|Simulation|tvb|visualisation|open source|analysis|supercomputer|brain model|neuroinformatics|image processing|the virtual brain
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5 5  = From MRI to Functional and Structural Connectivity =
6 6  
7 7  Neuroimaging data preprocessing pipeline
8 +
9 +== [[Pipeline Video Tutorial>>https://drive.google.com/file/d/1VcXf3GX3KoihF4UzJQXzuGL4XWoqj5Jr/view||rel="noopener noreferrer" target="_blank"]] ==
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8 8  )))
9 9  )))
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12 12  (((
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14 14  (((
15 -= What can I find here? =
36 +== 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
43 +
44 +== How do I use it? ==
45 +
46 +* the pipeline is implemented by three Docker containers (mrtrix3_connectome, fmriprep and tvb_converter)
47 +* the containers are executed on supercomputers and operated via IPython notebooks
48 +* Find the notebook by clicking on "Drive" in the left menu. The notebook is located in the folder "notebooks"
49 +* 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]]
50 +* To use the notebook, download it onto your local filesystem, create a new Collab and upload it there.
51 +* Then, head over to [[https:~~/~~/lab.ebrains.eu/>>url:https://lab.ebrains.eu/||rel="noopener noreferrer" target="_blank"]] to edit and run your notebook.
52 +* 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'"
53 +
54 +== Metadata ==
55 +
56 +* Partners: Charité Universitätsmedizin Berlin
57 +* Developers: Michael Schirner (michael.schirner@charite.de), Paul Triebkorn
58 +* Support: Petra Ritter (petra.ritter@charite.de)
59 +* Homepage: [[https:~~/~~/www.brainsimulation.org>>url:https://www.brainsimulation.org/]]
60 +* Documentation: [[https:~~/~~/drive.google.com/file/d/1VcXf3GX3KoihF4UzJQXzuGL4XWoqj5Jr/view>>https://drive.google.com/file/d/1VcXf3GX3KoihF4UzJQXzuGL4XWoqj5Jr/view]]
61 +* Download as Docker image~: [[https:~~/~~/hub.docker.com/r/thevirtualbrain/tvb_converter>>url:https://hub.docker.com/r/thevirtualbrain/tvb_converter]]
62 +* License: GPL3
63 +* Version: 1.0
22 22  )))
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TVB PIPELINE