Wiki source code of TVB PIPELINE

Version 25.1 by michaels on 2020/06/02 11:26
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michaels 7.1 5 = From MRI to Functional and Structural Connectivity =
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michaels 7.1 7 Neuroimaging data preprocessing pipeline
michaels 12.1 8
michaels 18.1 9 == [[Pipeline Video Tutorial>>https://drive.google.com/file/d/1VcXf3GX3KoihF4UzJQXzuGL4XWoqj5Jr/view||rel="noopener noreferrer" target="_blank"]] ==
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michaels 23.1 11 == [[Direct link to notebook>>https://drive.ebrains.eu/#my-libs/lib/42ac27a5-981e-4cf6-8ec5-d67b0c24bf09/notebooks||rel="noopener noreferrer" target="_blank"]] ==
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michaels 8.1 38 == What can I find here? ==
michaels 1.1 39
michaels 7.1 40 * an IPython notebook that describes how to
michaels 25.1 41 ** use the TVB processing pipeline on one of the associated supercomputers using PyUnicore
42 ** upload MRI data to the supercomputer
michaels 7.1 43 ** set up and run the pipeline
44 ** download processing results
michaels 8.1 45
michaels 25.1 46 == What does the TVB processing pipeline do? ==
47
48 After uploading MRI data to the supercomputer, the pipeline runs the three containers
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50 * [[bids/mrtrix3_connectome>>https://hub.docker.com/r/bids/mrtrix3_connectome||rel=" noopener noreferrer" target="_blank"]]
51 * [[poldracklab/fmriprep>>https://hub.docker.com/r/poldracklab/fmriprep||rel=" noopener noreferrer" target="_blank"]], and
52 * [[thevirtualbrain/tvb_converter>>https://hub.docker.com/r/thevirtualbrain/tvb_converter||rel=" noopener noreferrer" target="_blank"]]
53
54 The TVB Processing Pipeline takes multimodal MRI data sets (anatomical, functional and diffusion-weighted MRI) as input and generates SCs, region-average fMRI time series, FCs, brain surfaces, electrode positions, lead field matrices, and atlas parcellations as output. The pipeline performs preprocessing and distortion-correction on MRI data as well as white matter fiber bundle tractography on diffusion data. Outputs are formatted according to two data standards: a TVB-ready data set that can be directly used to simulate brain network models and the same output in BIDS format.
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michaels 8.1 56 == How do I use it? ==
57
58 * the pipeline is implemented by three Docker containers (mrtrix3_connectome, fmriprep and tvb_converter)
59 * the containers are executed on supercomputers and operated via IPython notebooks
60 * Find the notebook by clicking on "Drive" in the left menu. The notebook is located in the folder "notebooks"
michaels 10.1 61 * 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]]
michaels 8.1 62 * To use the notebook, download it onto your local filesystem, create a new Collab and upload it there.
michaels 10.1 63 * Then, head over to [[https:~~/~~/lab.ebrains.eu/>>url:https://lab.ebrains.eu/||rel="noopener noreferrer" target="_blank"]] to edit and run your notebook.
michaels 8.1 64 * 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'"
michaels 19.1 65
66 == Metadata ==
67
michaels 23.1 68 |=Category|tool
69 |=Tags|(((
70 * [[Simulaton>>url:https://services.humanbrainproject.eu/software-catalog/catalog/?ctx=97d59245-adce-42c4-8b50-d22587071fcd&ctxstate=search%2Ctvb]]
71 * [[TVB>>url:https://services.humanbrainproject.eu/software-catalog/catalog/?ctx=97d59245-adce-42c4-8b50-d22587071fcd&ctxstate=search%2Ctvb]]
72 * [[visualization>>url:https://services.humanbrainproject.eu/software-catalog/catalog/?ctx=97d59245-adce-42c4-8b50-d22587071fcd&ctxstate=search%2Ctvb]]
73 * [[open-source>>url:https://services.humanbrainproject.eu/software-catalog/catalog/?ctx=97d59245-adce-42c4-8b50-d22587071fcd&ctxstate=search%2Ctvb]]
74 * [[analysis>>url:https://services.humanbrainproject.eu/software-catalog/catalog/?ctx=97d59245-adce-42c4-8b50-d22587071fcd&ctxstate=search%2Ctvb]]
75 * [[supercomputers>>url:https://services.humanbrainproject.eu/software-catalog/catalog/?ctx=97d59245-adce-42c4-8b50-d22587071fcd&ctxstate=search%2Ctvb]]
76 * [[brain-model>>url:https://services.humanbrainproject.eu/software-catalog/catalog/?ctx=97d59245-adce-42c4-8b50-d22587071fcd&ctxstate=search%2Ctvb]]
77 * [[neuroinformatics>>url:https://services.humanbrainproject.eu/software-catalog/catalog/?ctx=97d59245-adce-42c4-8b50-d22587071fcd&ctxstate=search%2Ctvb]]
78 * [[image-segmentation>>url:https://services.humanbrainproject.eu/software-catalog/catalog/?ctx=97d59245-adce-42c4-8b50-d22587071fcd&ctxstate=search%2Ctvb]]
79 * [[simulation>>url:https://services.humanbrainproject.eu/software-catalog/catalog/?ctx=97d59245-adce-42c4-8b50-d22587071fcd&ctxstate=search%2Ctvb]]
80 * [[The-Virtual-Brain>>url:https://services.humanbrainproject.eu/software-catalog/catalog/?ctx=97d59245-adce-42c4-8b50-d22587071fcd&ctxstate=search%2Ctvb]]
81 )))
82 |=Partners|(((
83 * Charité Universitätsmedizin Berlin [[CHARITE>>url:https://services.humanbrainproject.eu/software-catalog/catalog/?ctx=97d59245-adce-42c4-8b50-d22587071fcd&ctxstate=search%2Ctvb]]
84 )))
85 |=Maintainers|(((
86 * [[Petra Ritter>>path:mailto:petra.ritter@charite.de]]
87 * [[Michael Schirner>>path:mailto:michael.schirner@charite.de]]
88 * [[Paul Triebkorn>>path:mailto:jan-paul.triebkorn@charite.de]]
89 )))
90 |=Contributors|(((
91 * [[Petra Ritter>>path:mailto:petra.ritter@charite.de]]
92 * [[Michael Schirner>>path:mailto:michael.schirner@charite.de]]
93 * [[Paul Triebkorn>>path:mailto:jan-paul.triebkorn@charite.de]]
94 )))
95 |=Homepage|[[https:~~/~~/www.brainsimulation.org>>url:https://www.brainsimulation.org/]]
96 |=Documentation|[[https:~~/~~/drive.google.com/file/d/1VcXf3GX3KoihF4UzJQXzuGL4XWoqj5Jr/view>>url:https://drive.google.com/file/d/1VcXf3GX3KoihF4UzJQXzuGL4XWoqj5Jr/view]]
97 |=Support|[[petra.ritter@charite.de>>path:mailto:petra.ritter@charite.de]]
98 |=Source Code|[[https:~~/~~/hub.docker.com/r/thevirtualbrain/tvb_converter>>url:https://hub.docker.com/r/thevirtualbrain/tvb_converter]]
99 |=Download Page|[[https:~~/~~/hub.docker.com/r/thevirtualbrain/tvb_converter>>url:https://hub.docker.com/r/thevirtualbrain/tvb_converter]]
100 |=License|GPLv3
101 |=Current Version|1.0
102 |=All Versions|(((
103 * 1.0
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michaels 20.1 105
michaels 24.1 106 === ===
michaels 23.1 107
michaels 21.1 108 == Publications on TVB/brain model preprocessing ==
michaels 20.1 109
110 * [[https:~~/~~/www.ncbi.nlm.nih.gov/pubmed/25837600>>url:https://www.ncbi.nlm.nih.gov/pubmed/25837600]]
111 * [[https:~~/~~/www.ncbi.nlm.nih.gov/pubmed/27480624>>url:https://www.ncbi.nlm.nih.gov/pubmed/27480624]]
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117 {{box title="**Contents**"}}
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TVB PIPELINE