Wiki source code of TVB PIPELINE
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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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| 9 | == [[Pipeline Video Tutorial>>https://drive.google.com/file/d/1VcXf3GX3KoihF4UzJQXzuGL4XWoqj5Jr/view||rel="noopener noreferrer" target="_blank"]] == | ||
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| 36 | == What can I find here? == | ||
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| 38 | * an IPython notebook that describes how to | ||
| 39 | ** use the TVB pipeline on one of the associated supercomputers using PyUnicore | ||
| 40 | ** upload model data to the supercomputer | ||
| 41 | ** set up and run the pipeline | ||
| 42 | ** download processing results | ||
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| 44 | == How do I use it? == | ||
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| 46 | * the pipeline is implemented by three Docker containers (mrtrix3_connectome, fmriprep and tvb_converter) | ||
| 47 | * the containers are executed on supercomputers and operated via IPython notebooks | ||
| 48 | * Find the notebook by clicking on "Drive" in the left menu. The notebook is located in the folder "notebooks" | ||
| 49 | * 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]] | ||
| 50 | * To use the notebook, download it onto your local filesystem, create a new Collab and upload it there. | ||
| 51 | * Then, head over to [[https:~~/~~/lab.ebrains.eu/>>url:https://lab.ebrains.eu/||rel="noopener noreferrer" target="_blank"]] to edit and run your notebook. | ||
| 52 | * 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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| 58 | {{box title="**Contents**"}} | ||
| 59 | {{toc/}} | ||
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