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 17.1
edited by michaels
on 2020/05/06 13:44
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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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 +[[image:8677353.png||style="float:left"]]
10 +
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34 +== [[Pipeline Video Tutorial>>https://drive.google.com/file/d/1VcXf3GX3KoihF4UzJQXzuGL4XWoqj5Jr/view||rel="noopener noreferrer" target="_blank"]] ==
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15 -= What can I find here? =
42 +== 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
44 +* an IPython notebook that describes how to
45 +** use the TVB pipeline on one of the associated supercomputers using PyUnicore
46 +** upload model data to the supercomputer
47 +** set up and run the pipeline
48 +** download processing results
20 20  
21 -= Who has access? =
50 +== How do I use it? ==
22 22  
23 -Describe the audience of this collab.
52 +* the pipeline is implemented by three Docker containers (mrtrix3_connectome, fmriprep and tvb_converter)
53 +* the containers are executed on supercomputers and operated via IPython notebooks
54 +* Find the notebook by clicking on "Drive" in the left menu. The notebook is located in the folder "notebooks"
55 +* 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]]
56 +* To use the notebook, download it onto your local filesystem, create a new Collab and upload it there.
57 +* Then, head over to [[https:~~/~~/lab.ebrains.eu/>>url:https://lab.ebrains.eu/||rel="noopener noreferrer" target="_blank"]] to edit and run your notebook.
58 +* 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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TVB PIPELINE