Changes for page TVB PIPELINE

Last modified by ldomide on 2024/05/20 08:56
From version 8.1
edited by michaels
on 2020/05/06 09:19
Change comment: There is no comment for this version
To version 25.1
edited by michaels
on 2020/06/02 11:26
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 +== ==
25 +
26 +== ==
27 +
28 +== ==
29 +
30 +== ==
8 8  )))
9 9  )))
10 10  
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15 15  == What can I find here? ==
16 16  
17 17  * an IPython notebook that describes how to
18 -** use the TVB pipeline on one of the associated supercomputers using PyUnicore
19 -** upload model data to the supercomputer
41 +** use the TVB processing pipeline on one of the associated supercomputers using PyUnicore
42 +** upload MRI data to the supercomputer
20 20  ** set up and run the pipeline
21 21  ** download processing results
22 22  
46 +== What does the TVB processing pipeline do? ==
23 23  
48 +After uploading MRI data to the supercomputer, the pipeline runs the three containers
49 +
50 +* [[bids/mrtrix3_connectome>>https://hub.docker.com/r/bids/mrtrix3_connectome||rel=" noopener noreferrer" target="_blank"]]
51 +* [[poldracklab/fmriprep>>https://hub.docker.com/r/poldracklab/fmriprep||rel=" noopener noreferrer" target="_blank"]], and
52 +* [[thevirtualbrain/tvb_converter>>https://hub.docker.com/r/thevirtualbrain/tvb_converter||rel=" noopener noreferrer" target="_blank"]]
53 +
54 +The TVB Processing Pipeline takes multimodal MRI data sets (anatomical, functional and diffusion-weighted MRI) as input and generates SCs, region-average fMRI time series, FCs, brain surfaces, electrode positions, lead field matrices, and atlas parcellations as output. The pipeline performs preprocessing and distortion-correction on MRI data as well as white matter fiber bundle tractography on diffusion data. Outputs are formatted according to two data standards: a TVB-ready data set that can be directly used to simulate brain network models and the same output in BIDS format.
55 +
24 24  == How do I use it? ==
25 25  
26 26  * the pipeline is implemented by three Docker containers (mrtrix3_connectome, fmriprep and tvb_converter)
27 27  * the containers are executed on supercomputers and operated via IPython notebooks
28 28  * Find the notebook by clicking on "Drive" in the left menu. The notebook is located in the folder "notebooks"
61 +* 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]]
29 29  * To use the notebook, download it onto your local filesystem, create a new Collab and upload it there.
30 -* Then, head over to [[https:~~/~~/lab.ebrains.eu/>>url:https://lab.ebrains.eu/]] to edit and run your notebook.
63 +* Then, head over to [[https:~~/~~/lab.ebrains.eu/>>url:https://lab.ebrains.eu/||rel="noopener noreferrer" target="_blank"]] to edit and run your notebook.
31 31  * 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'"
65 +
66 +== Metadata ==
67 +
68 +|=Category|tool
69 +|=Tags|(((
70 +* [[Simulaton>>url:https://services.humanbrainproject.eu/software-catalog/catalog/?ctx=97d59245-adce-42c4-8b50-d22587071fcd&ctxstate=search%2Ctvb]]
71 +* [[TVB>>url:https://services.humanbrainproject.eu/software-catalog/catalog/?ctx=97d59245-adce-42c4-8b50-d22587071fcd&ctxstate=search%2Ctvb]]
72 +* [[visualization>>url:https://services.humanbrainproject.eu/software-catalog/catalog/?ctx=97d59245-adce-42c4-8b50-d22587071fcd&ctxstate=search%2Ctvb]]
73 +* [[open-source>>url:https://services.humanbrainproject.eu/software-catalog/catalog/?ctx=97d59245-adce-42c4-8b50-d22587071fcd&ctxstate=search%2Ctvb]]
74 +* [[analysis>>url:https://services.humanbrainproject.eu/software-catalog/catalog/?ctx=97d59245-adce-42c4-8b50-d22587071fcd&ctxstate=search%2Ctvb]]
75 +* [[supercomputers>>url:https://services.humanbrainproject.eu/software-catalog/catalog/?ctx=97d59245-adce-42c4-8b50-d22587071fcd&ctxstate=search%2Ctvb]]
76 +* [[brain-model>>url:https://services.humanbrainproject.eu/software-catalog/catalog/?ctx=97d59245-adce-42c4-8b50-d22587071fcd&ctxstate=search%2Ctvb]]
77 +* [[neuroinformatics>>url:https://services.humanbrainproject.eu/software-catalog/catalog/?ctx=97d59245-adce-42c4-8b50-d22587071fcd&ctxstate=search%2Ctvb]]
78 +* [[image-segmentation>>url:https://services.humanbrainproject.eu/software-catalog/catalog/?ctx=97d59245-adce-42c4-8b50-d22587071fcd&ctxstate=search%2Ctvb]]
79 +* [[simulation>>url:https://services.humanbrainproject.eu/software-catalog/catalog/?ctx=97d59245-adce-42c4-8b50-d22587071fcd&ctxstate=search%2Ctvb]]
80 +* [[The-Virtual-Brain>>url:https://services.humanbrainproject.eu/software-catalog/catalog/?ctx=97d59245-adce-42c4-8b50-d22587071fcd&ctxstate=search%2Ctvb]]
32 32  )))
82 +|=Partners|(((
83 +* Charité Universitätsmedizin Berlin [[CHARITE>>url:https://services.humanbrainproject.eu/software-catalog/catalog/?ctx=97d59245-adce-42c4-8b50-d22587071fcd&ctxstate=search%2Ctvb]]
84 +)))
85 +|=Maintainers|(((
86 +* [[Petra Ritter>>path:mailto:petra.ritter@charite.de]]
87 +* [[Michael Schirner>>path:mailto:michael.schirner@charite.de]]
88 +* [[Paul Triebkorn>>path:mailto:jan-paul.triebkorn@charite.de]]
89 +)))
90 +|=Contributors|(((
91 +* [[Petra Ritter>>path:mailto:petra.ritter@charite.de]]
92 +* [[Michael Schirner>>path:mailto:michael.schirner@charite.de]]
93 +* [[Paul Triebkorn>>path:mailto:jan-paul.triebkorn@charite.de]]
94 +)))
95 +|=Homepage|[[https:~~/~~/www.brainsimulation.org>>url:https://www.brainsimulation.org/]]
96 +|=Documentation|[[https:~~/~~/drive.google.com/file/d/1VcXf3GX3KoihF4UzJQXzuGL4XWoqj5Jr/view>>url:https://drive.google.com/file/d/1VcXf3GX3KoihF4UzJQXzuGL4XWoqj5Jr/view]]
97 +|=Support|[[petra.ritter@charite.de>>path:mailto:petra.ritter@charite.de]]
98 +|=Source Code|[[https:~~/~~/hub.docker.com/r/thevirtualbrain/tvb_converter>>url:https://hub.docker.com/r/thevirtualbrain/tvb_converter]]
99 +|=Download Page|[[https:~~/~~/hub.docker.com/r/thevirtualbrain/tvb_converter>>url:https://hub.docker.com/r/thevirtualbrain/tvb_converter]]
100 +|=License|GPLv3
101 +|=Current Version|1.0
102 +|=All Versions|(((
103 +* 1.0
104 +)))
33 33  
106 +=== ===
34 34  
108 +== Publications on TVB/brain model preprocessing ==
109 +
110 +* [[https:~~/~~/www.ncbi.nlm.nih.gov/pubmed/25837600>>url:https://www.ncbi.nlm.nih.gov/pubmed/25837600]]
111 +* [[https:~~/~~/www.ncbi.nlm.nih.gov/pubmed/27480624>>url:https://www.ncbi.nlm.nih.gov/pubmed/27480624]]
112 +)))
113 +
114 +
35 35  (% class="col-xs-12 col-sm-4" %)
36 36  (((
37 37  {{box title="**Contents**"}}
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TVB PIPELINE