Changes for page TVB PIPELINE

Last modified by ldomide on 2024/05/20 08:56
From version 6.1
edited by michaels
on 2020/05/04 08:16
Change comment: There is no comment for this version
To version 24.1
edited by michaels
on 2020/05/07 14:05
Change comment: There is no comment for this version

Summary

Details

Page properties
Tags
... ... @@ -1,0 +1,1 @@
1 +tool|CHARITE|Simulation|tvb|visualisation|open source|analysis|supercomputer|brain model|neuroinformatics|image processing|the virtual brain
Content
... ... @@ -2,9 +2,32 @@
2 2  (((
3 3  (% class="container" %)
4 4  (((
5 -= My Collab's Extended Title =
5 += From MRI to Functional and Structural Connectivity =
6 6  
7 -My collab's subtitle
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"]] ==
12 +
13 +
14 +[[image:8677353.png||style="float:left"]]
15 +
16 +== ==
17 +
18 +== ==
19 +
20 +== ==
21 +
22 +== ==
23 +
24 +== ==
25 +
26 +== ==
27 +
28 +== ==
29 +
30 +== ==
8 8  )))
9 9  )))
10 10  
... ... @@ -12,18 +12,73 @@
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 -* Notice how the table of contents on the right
18 -* is automatically updated
19 -* to hold this page's headers
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
20 20  
21 -= Who has access? =
46 +== How do I use it? ==
22 22  
23 -Describe the audience of this collab.
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]]
24 24  )))
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 +)))
25 25  
96 +=== ===
26 26  
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 +
27 27  (% class="col-xs-12 col-sm-4" %)
28 28  (((
29 29  {{box title="**Contents**"}}
8677353.png
Author
... ... @@ -1,0 +1,1 @@
1 +XWiki.michaels
Size
... ... @@ -1,0 +1,1 @@
1 +227.9 KB
Content
8d975cf4-13ec-4a6d-9fd9-064bd1fac7b0.jpeg
Author
... ... @@ -1,0 +1,1 @@
1 +XWiki.michaels
Size
... ... @@ -1,0 +1,1 @@
1 +107.1 KB
Content
Public

TVB PIPELINE