Changes for page TVB PIPELINE

Last modified by ldomide on 2024/05/20 08:56
From version 20.1
edited by michaels
on 2020/05/06 14:11
Change comment: There is no comment for this version
To version 7.1
edited by michaels
on 2020/05/06 09:11
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
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9 -== [[Pipeline Video Tutorial>>https://drive.google.com/file/d/1VcXf3GX3KoihF4UzJQXzuGL4XWoqj5Jr/view||rel="noopener noreferrer" target="_blank"]] ==
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29 29  )))
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36 -== What can I find here? ==
15 += What can I find here? =
37 37  
38 38  * an IPython notebook that describes how to
39 39  ** use the TVB pipeline on one of the associated supercomputers using PyUnicore
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40 40  ** upload model data to the supercomputer
41 41  ** set up and run the pipeline
42 42  ** 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
64 -
65 -
66 -== Publications on TVB preprocessing pipelines ==
67 -
68 -* [[https:~~/~~/www.ncbi.nlm.nih.gov/pubmed/25837600>>url:https://www.ncbi.nlm.nih.gov/pubmed/25837600]]
69 -* [[https:~~/~~/www.ncbi.nlm.nih.gov/pubmed/27480624>>url:https://www.ncbi.nlm.nih.gov/pubmed/27480624]]
70 70  )))
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TVB PIPELINE