Wiki source code of TVB PIPELINE

Version 15.1 by michaels on 2020/05/06 13:44
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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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12 == [[Pipeline Video Tutorial>>https://drive.google.com/file/d/1VcXf3GX3KoihF4UzJQXzuGL4XWoqj5Jr/view||target="_blank"]] ==
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20 == What can I find here? ==
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22 * an IPython notebook that describes how to
23 ** use the TVB pipeline on one of the associated supercomputers using PyUnicore
24 ** upload model data to the supercomputer
25 ** set up and run the pipeline
26 ** download processing results
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28 == How do I use it? ==
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30 * the pipeline is implemented by three Docker containers (mrtrix3_connectome, fmriprep and tvb_converter)
31 * the containers are executed on supercomputers and operated via IPython notebooks
32 * Find the notebook by clicking on "Drive" in the left menu. The notebook is located in the folder "notebooks"
33 * 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]]
34 * To use the notebook, download it onto your local filesystem, create a new Collab and upload it there.
35 * Then, head over to [[https:~~/~~/lab.ebrains.eu/>>url:https://lab.ebrains.eu/||rel="noopener noreferrer" target="_blank"]] to edit and run your notebook.
36 * 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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42 {{box title="**Contents**"}}
43 {{toc/}}
44 {{/box}}
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Public

TVB PIPELINE