Wiki source code of TVB PIPELINE
Hide last authors
| author | version | line-number | content |
|---|---|---|---|
 |
1.1 | 1 | (% class="jumbotron" %) |
| 2 | ((( | ||
| 3 | (% class="container" %) | ||
| 4 | ((( | ||
| |
7.1 | 5 | = From MRI to Functional and Structural Connectivity = |
| |
1.1 | 6 | |
| |
7.1 | 7 | Neuroimaging data preprocessing pipeline |
| |
12.1 | 8 | |
| |
18.1 | 9 | == [[Pipeline Video Tutorial>>https://drive.google.com/file/d/1VcXf3GX3KoihF4UzJQXzuGL4XWoqj5Jr/view||rel="noopener noreferrer" target="_blank"]] == |
| |
12.1 | 10 | |
| |
22.1 | 11 | == [[Direct link to notebook>>https://drive.ebrains.eu/#my-libs/lib/42ac27a5-981e-4cf6-8ec5-d67b0c24bf09/notebooks||target="_blank"]] == |
| |
16.1 | 12 | |
| |
22.1 | 13 | |
| |
18.1 | 14 | [[image:8677353.png||style="float:left"]] |
| |
16.1 | 15 | |
| 16 | == == | ||
| 17 | |||
| 18 | == == | ||
| 19 | |||
| |
17.1 | 20 | == == |
| 21 | |||
| 22 | == == | ||
| 23 | |||
| 24 | == == | ||
| 25 | |||
| |
16.1 | 26 | == == |
| 27 | |||
| 28 | == == | ||
| 29 | |||
| 30 | == == | ||
| |
1.1 | 31 | ))) |
| 32 | ))) | ||
| 33 | |||
| 34 | (% class="row" %) | ||
| 35 | ((( | ||
| 36 | (% class="col-xs-12 col-sm-8" %) | ||
| 37 | ((( | ||
| |
8.1 | 38 | == What can I find here? == |
| |
1.1 | 39 | |
| |
7.1 | 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 | ||
| |
8.1 | 45 | |
| 46 | == How do I use it? == | ||
| 47 | |||
| 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" | ||
| |
10.1 | 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]] |
| |
8.1 | 52 | * To use the notebook, download it onto your local filesystem, create a new Collab and upload it there. |
| |
10.1 | 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. |
| |
8.1 | 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'" |
| |
19.1 | 55 | |
| 56 | == Metadata == | ||
| 57 | |||
| 58 | * Partners: Charité Universitätsmedizin Berlin | ||
| 59 | * Developers: Michael Schirner (michael.schirner@charite.de), Paul Triebkorn | ||
| 60 | * Support: Petra Ritter (petra.ritter@charite.de) | ||
| 61 | * Homepage: [[https:~~/~~/www.brainsimulation.org>>url:https://www.brainsimulation.org/]] | ||
| 62 | * Documentation: [[https:~~/~~/drive.google.com/file/d/1VcXf3GX3KoihF4UzJQXzuGL4XWoqj5Jr/view>>https://drive.google.com/file/d/1VcXf3GX3KoihF4UzJQXzuGL4XWoqj5Jr/view]] | ||
| 63 | * Download as Docker image~: [[https:~~/~~/hub.docker.com/r/thevirtualbrain/tvb_converter>>url:https://hub.docker.com/r/thevirtualbrain/tvb_converter]] | ||
| 64 | * License: GPL3 | ||
| 65 | * Version: 1.0 | ||
| |
20.1 | 66 | |
| |
21.1 | 67 | == Publications on TVB/brain model preprocessing == |
| |
20.1 | 68 | |
| 69 | * [[https:~~/~~/www.ncbi.nlm.nih.gov/pubmed/25837600>>url:https://www.ncbi.nlm.nih.gov/pubmed/25837600]] | ||
| 70 | * [[https:~~/~~/www.ncbi.nlm.nih.gov/pubmed/27480624>>url:https://www.ncbi.nlm.nih.gov/pubmed/27480624]] | ||
| |
1.1 | 71 | ))) |
| 72 | |||
| 73 | |||
| 74 | (% class="col-xs-12 col-sm-4" %) | ||
| 75 | ((( | ||
| 76 | {{box title="**Contents**"}} | ||
| 77 | {{toc/}} | ||
| 78 | {{/box}} | ||
| 79 | |||
| 80 | |||
| 81 | ))) | ||
| 82 | ))) |