Wiki source code of TVB PIPELINE

Version 23.1 by michaels on 2020/05/06 15:09
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5 = From MRI to Functional and Structural Connectivity =
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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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11 == [[Direct link to notebook>>https://drive.ebrains.eu/#my-libs/lib/42ac27a5-981e-4cf6-8ec5-d67b0c24bf09/notebooks||rel="noopener noreferrer" target="_blank"]] ==
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38 == What can I find here? ==
39
40 * an IPython notebook that describes how to
41 ** use the TVB pipeline on one of the associated supercomputers using PyUnicore
42 ** upload model data to the supercomputer
43 ** set up and run the pipeline
44 ** download processing results
45
46 == How do I use it? ==
47
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
50 * Find the notebook by clicking on "Drive" in the left menu. The notebook is located in the folder "notebooks"
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 * To use the notebook, download it onto your local filesystem, create a new Collab and upload it there.
53 * Then, head over to [[https:~~/~~/lab.ebrains.eu/>>url:https://lab.ebrains.eu/||rel="noopener noreferrer" target="_blank"]] to edit and run your notebook.
54 * 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'"
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56 == Metadata ==
57
58 |=Category|tool
59 |=Tags|(((
60 * [[Simulaton>>url:https://services.humanbrainproject.eu/software-catalog/catalog/?ctx=97d59245-adce-42c4-8b50-d22587071fcd&ctxstate=search%2Ctvb]]
61 * [[TVB>>url:https://services.humanbrainproject.eu/software-catalog/catalog/?ctx=97d59245-adce-42c4-8b50-d22587071fcd&ctxstate=search%2Ctvb]]
62 * [[visualization>>url:https://services.humanbrainproject.eu/software-catalog/catalog/?ctx=97d59245-adce-42c4-8b50-d22587071fcd&ctxstate=search%2Ctvb]]
63 * [[open-source>>url:https://services.humanbrainproject.eu/software-catalog/catalog/?ctx=97d59245-adce-42c4-8b50-d22587071fcd&ctxstate=search%2Ctvb]]
64 * [[analysis>>url:https://services.humanbrainproject.eu/software-catalog/catalog/?ctx=97d59245-adce-42c4-8b50-d22587071fcd&ctxstate=search%2Ctvb]]
65 * [[supercomputers>>url:https://services.humanbrainproject.eu/software-catalog/catalog/?ctx=97d59245-adce-42c4-8b50-d22587071fcd&ctxstate=search%2Ctvb]]
66 * [[brain-model>>url:https://services.humanbrainproject.eu/software-catalog/catalog/?ctx=97d59245-adce-42c4-8b50-d22587071fcd&ctxstate=search%2Ctvb]]
67 * [[neuroinformatics>>url:https://services.humanbrainproject.eu/software-catalog/catalog/?ctx=97d59245-adce-42c4-8b50-d22587071fcd&ctxstate=search%2Ctvb]]
68 * [[image-segmentation>>url:https://services.humanbrainproject.eu/software-catalog/catalog/?ctx=97d59245-adce-42c4-8b50-d22587071fcd&ctxstate=search%2Ctvb]]
69 * [[simulation>>url:https://services.humanbrainproject.eu/software-catalog/catalog/?ctx=97d59245-adce-42c4-8b50-d22587071fcd&ctxstate=search%2Ctvb]]
70 * [[The-Virtual-Brain>>url:https://services.humanbrainproject.eu/software-catalog/catalog/?ctx=97d59245-adce-42c4-8b50-d22587071fcd&ctxstate=search%2Ctvb]]
71 )))
72 |=Partners|(((
73 * Charité Universitätsmedizin Berlin [[CHARITE>>url:https://services.humanbrainproject.eu/software-catalog/catalog/?ctx=97d59245-adce-42c4-8b50-d22587071fcd&ctxstate=search%2Ctvb]]
74 )))
75 |=Maintainers|(((
76 * [[Petra Ritter>>path:mailto:petra.ritter@charite.de]]
77 * [[Michael Schirner>>path:mailto:michael.schirner@charite.de]]
78 * [[Paul Triebkorn>>path:mailto:jan-paul.triebkorn@charite.de]]
79 )))
80 |=Contributors|(((
81 * [[Petra Ritter>>path:mailto:petra.ritter@charite.de]]
82 * [[Michael Schirner>>path:mailto:michael.schirner@charite.de]]
83 * [[Paul Triebkorn>>path:mailto:jan-paul.triebkorn@charite.de]]
84 )))
85 |=Homepage|[[https:~~/~~/www.brainsimulation.org>>url:https://www.brainsimulation.org/]]
86 |=Documentation|[[https:~~/~~/drive.google.com/file/d/1VcXf3GX3KoihF4UzJQXzuGL4XWoqj5Jr/view>>url:https://drive.google.com/file/d/1VcXf3GX3KoihF4UzJQXzuGL4XWoqj5Jr/view]]
87 |=Support|[[petra.ritter@charite.de>>path:mailto:petra.ritter@charite.de]]
88 |=Source Code|[[https:~~/~~/hub.docker.com/r/thevirtualbrain/tvb_converter>>url:https://hub.docker.com/r/thevirtualbrain/tvb_converter]]
89 |=Download Page|[[https:~~/~~/hub.docker.com/r/thevirtualbrain/tvb_converter>>url:https://hub.docker.com/r/thevirtualbrain/tvb_converter]]
90 |=License|GPLv3
91 |=Current Version|1.0
92 |=All Versions|(((
93 * 1.0
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95
96 === Activities ===
97
98 == Publications on TVB/brain model preprocessing ==
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100 * [[https:~~/~~/www.ncbi.nlm.nih.gov/pubmed/25837600>>url:https://www.ncbi.nlm.nih.gov/pubmed/25837600]]
101 * [[https:~~/~~/www.ncbi.nlm.nih.gov/pubmed/27480624>>url:https://www.ncbi.nlm.nih.gov/pubmed/27480624]]
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107 {{box title="**Contents**"}}
108 {{toc/}}
109 {{/box}}
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Public

TVB PIPELINE