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 23.1
edited by michaels
on 2020/05/06 15:09
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"]] ==
10 +
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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14 +[[image:8677353.png||style="float:left"]]
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16 +== ==
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18 +== ==
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20 +== ==
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22 +== ==
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24 +== ==
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26 +== ==
27 +
28 +== ==
29 +
30 +== ==
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? =
38 +== 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
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'"
55 +
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]]
22 22  )))
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
94 +)))
23 23  
96 +=== Activities ===
24 24  
98 +== Publications on TVB/brain model preprocessing ==
99 +
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]]
102 +)))
103 +
104 +
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26 26  (((
27 27  {{box title="**Contents**"}}
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TVB PIPELINE