Wiki source code of TVB PIPELINE
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7.1 | 5 | = From MRI to Functional and Structural Connectivity = |
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7.1 | 7 | Neuroimaging data preprocessing pipeline |
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18.1 | 9 | == [[Pipeline Video Tutorial>>https://drive.google.com/file/d/1VcXf3GX3KoihF4UzJQXzuGL4XWoqj5Jr/view||rel="noopener noreferrer" target="_blank"]] == |
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18.1 | 12 | [[image:8677353.png||style="float:left"]] |
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8.1 | 36 | == What can I find here? == |
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1.1 | 37 | |
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7.1 | 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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8.1 | 43 | |
| 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" | ||
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10.1 | 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]] |
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8.1 | 50 | * To use the notebook, download it onto your local filesystem, create a new Collab and upload it there. |
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10.1 | 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. |
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8.1 | 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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19.1 | 53 | |
| 54 | == Metadata == | ||
| 55 | |||
| 56 | * Partners: Charité Universitätsmedizin Berlin | ||
| 57 | * Developers: Michael Schirner (michael.schirner@charite.de), Paul Triebkorn | ||
| 58 | * Support: Petra Ritter (petra.ritter@charite.de) | ||
| 59 | * Homepage: [[https:~~/~~/www.brainsimulation.org>>url:https://www.brainsimulation.org/]] | ||
| 60 | * Documentation: [[https:~~/~~/drive.google.com/file/d/1VcXf3GX3KoihF4UzJQXzuGL4XWoqj5Jr/view>>https://drive.google.com/file/d/1VcXf3GX3KoihF4UzJQXzuGL4XWoqj5Jr/view]] | ||
| 61 | * Download as Docker image~: [[https:~~/~~/hub.docker.com/r/thevirtualbrain/tvb_converter>>url:https://hub.docker.com/r/thevirtualbrain/tvb_converter]] | ||
| 62 | * License: GPL3 | ||
| 63 | * Version: 1.0 | ||
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20.1 | 64 | |
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| 66 | == Publications on TVB preprocessing pipelines == | ||
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| 68 | * [[https:~~/~~/www.ncbi.nlm.nih.gov/pubmed/25837600>>url:https://www.ncbi.nlm.nih.gov/pubmed/25837600]] | ||
| 69 | * [[https:~~/~~/www.ncbi.nlm.nih.gov/pubmed/27480624>>url:https://www.ncbi.nlm.nih.gov/pubmed/27480624]] | ||
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| 75 | {{box title="**Contents**"}} | ||
| 76 | {{toc/}} | ||
| 77 | {{/box}} | ||
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