Changes for page TVB PIPELINE

Last modified by ldomide on 2024/05/20 08:56
From version 32.1
edited by michaels
on 2020/06/26 12:24
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To version 16.1
edited by michaels
on 2020/05/06 13:44
Change comment: There is no comment for this version

Summary

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5 -= TVB Image Processing Pipeline With MINDS annotated Outputs =
5 += From MRI to Functional and Structural Connectivity =
6 6  
7 -== [[Pipeline Video Tutorial>>https://drive.google.com/file/d/1VcXf3GX3KoihF4UzJQXzuGL4XWoqj5Jr/view||rel="noopener noreferrer" target="_blank"]] ==
7 +Neuroimaging data preprocessing pipeline
8 8  
9 -== [[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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32 +== [[Pipeline Video Tutorial>>https://drive.google.com/file/d/1VcXf3GX3KoihF4UzJQXzuGL4XWoqj5Jr/view||rel="noopener noreferrer" target="_blank"]] ==
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16 16  
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21 21  == What can I find here? ==
22 22  
23 23  * an IPython notebook that describes how to
24 -** use the TVB processing pipeline on one of the associated supercomputers using PyUnicore
25 -** upload MRI data to the supercomputer
43 +** use the TVB pipeline on one of the associated supercomputers using PyUnicore
44 +** upload model data to the supercomputer
26 26  ** set up and run the pipeline
27 27  ** download processing results
28 28  
29 -== What does the TVB processing pipeline do? ==
30 -
31 -After uploading MRI data to the supercomputer, the pipeline runs the three containers
32 -
33 -* [[bids/mrtrix3_connectome>>https://hub.docker.com/r/bids/mrtrix3_connectome||rel="noopener noreferrer" target="_blank"]]
34 -* [[poldracklab/fmriprep>>https://hub.docker.com/r/poldracklab/fmriprep||rel="noopener noreferrer" target="_blank"]], and
35 -* [[thevirtualbrain/tvb_converter>>https://hub.docker.com/r/thevirtualbrain/tvb_converter||rel="noopener noreferrer" target="_blank"]]
36 -
37 -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.
38 -
39 39  == How do I use it? ==
40 40  
41 41  * the pipeline is implemented by three Docker containers (mrtrix3_connectome, fmriprep and tvb_converter)
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45 45  * To use the notebook, download it onto your local filesystem, create a new Collab and upload it there.
46 46  * Then, head over to [[https:~~/~~/lab.ebrains.eu/>>url:https://lab.ebrains.eu/||rel="noopener noreferrer" target="_blank"]] to edit and run your notebook.
47 47  * 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'"
48 -
49 -== Metadata ==
50 -
51 -|=Category|tool
52 -|=Tags|(((
53 -* [[Simulaton>>url:https://services.humanbrainproject.eu/software-catalog/catalog/?ctx=97d59245-adce-42c4-8b50-d22587071fcd&ctxstate=search%2Ctvb]]
54 -* [[TVB>>url:https://services.humanbrainproject.eu/software-catalog/catalog/?ctx=97d59245-adce-42c4-8b50-d22587071fcd&ctxstate=search%2Ctvb]]
55 -* [[visualization>>url:https://services.humanbrainproject.eu/software-catalog/catalog/?ctx=97d59245-adce-42c4-8b50-d22587071fcd&ctxstate=search%2Ctvb]]
56 -* [[open-source>>url:https://services.humanbrainproject.eu/software-catalog/catalog/?ctx=97d59245-adce-42c4-8b50-d22587071fcd&ctxstate=search%2Ctvb]]
57 -* [[analysis>>url:https://services.humanbrainproject.eu/software-catalog/catalog/?ctx=97d59245-adce-42c4-8b50-d22587071fcd&ctxstate=search%2Ctvb]]
58 -* [[supercomputers>>url:https://services.humanbrainproject.eu/software-catalog/catalog/?ctx=97d59245-adce-42c4-8b50-d22587071fcd&ctxstate=search%2Ctvb]]
59 -* [[brain-model>>url:https://services.humanbrainproject.eu/software-catalog/catalog/?ctx=97d59245-adce-42c4-8b50-d22587071fcd&ctxstate=search%2Ctvb]]
60 -* [[neuroinformatics>>url:https://services.humanbrainproject.eu/software-catalog/catalog/?ctx=97d59245-adce-42c4-8b50-d22587071fcd&ctxstate=search%2Ctvb]]
61 -* [[image-segmentation>>url:https://services.humanbrainproject.eu/software-catalog/catalog/?ctx=97d59245-adce-42c4-8b50-d22587071fcd&ctxstate=search%2Ctvb]]
62 -* [[simulation>>url:https://services.humanbrainproject.eu/software-catalog/catalog/?ctx=97d59245-adce-42c4-8b50-d22587071fcd&ctxstate=search%2Ctvb]]
63 -* [[The-Virtual-Brain>>url:https://services.humanbrainproject.eu/software-catalog/catalog/?ctx=97d59245-adce-42c4-8b50-d22587071fcd&ctxstate=search%2Ctvb]]
64 64  )))
65 -|=Partners|(((
66 -* Charité Universitätsmedizin Berlin [[CHARITE>>url:https://services.humanbrainproject.eu/software-catalog/catalog/?ctx=97d59245-adce-42c4-8b50-d22587071fcd&ctxstate=search%2Ctvb]]
67 -)))
68 -|=Maintainers|(((
69 -* [[Petra Ritter>>path:mailto:petra.ritter@charite.de]]
70 -* [[Michael Schirner>>path:mailto:michael.schirner@charite.de]]
71 -* [[Paul Triebkorn>>path:mailto:jan-paul.triebkorn@charite.de]]
72 -)))
73 -|=Contributors|(((
74 -* [[Petra Ritter>>path:mailto:petra.ritter@charite.de]]
75 -* [[Michael Schirner>>path:mailto:michael.schirner@charite.de]]
76 -* [[Paul Triebkorn>>path:mailto:jan-paul.triebkorn@charite.de]]
77 -)))
78 -|=Homepage|[[https:~~/~~/www.brainsimulation.org>>url:https://www.brainsimulation.org/]]
79 -|=Documentation|[[https:~~/~~/drive.google.com/file/d/1VcXf3GX3KoihF4UzJQXzuGL4XWoqj5Jr/view>>url:https://drive.google.com/file/d/1VcXf3GX3KoihF4UzJQXzuGL4XWoqj5Jr/view]]
80 -|=Support|[[petra.ritter@charite.de>>path:mailto:petra.ritter@charite.de]]
81 -|=Source Code|[[https:~~/~~/hub.docker.com/r/thevirtualbrain/tvb_converter>>url:https://hub.docker.com/r/thevirtualbrain/tvb_converter]]
82 -|=Download Page|[[https:~~/~~/hub.docker.com/r/thevirtualbrain/tvb_converter>>url:https://hub.docker.com/r/thevirtualbrain/tvb_converter]]
83 -|=License|GPLv3
84 -|=Current Version|1.0
85 -|=All Versions|(((
86 -* 1.0
87 -)))
88 88  
89 -=== ===
90 90  
91 -== Publications on TVB/brain model preprocessing ==
92 -
93 -* [[https:~~/~~/www.ncbi.nlm.nih.gov/pubmed/25837600>>url:https://www.ncbi.nlm.nih.gov/pubmed/25837600]]
94 -* [[https:~~/~~/www.ncbi.nlm.nih.gov/pubmed/27480624>>url:https://www.ncbi.nlm.nih.gov/pubmed/27480624]]
95 -
96 -== Citing this work ==
97 -
98 -
99 -When using this pipeline for published work, please acknowledge MRtrix3, MRtrix3_connectome (R. Smith & Connelly, 2019; Tournier et al., 2019) and fmriprep (Esteban et al., 2019).
100 -
101 -
102 -Esteban, O., Markiewicz, C. J., Blair, R. W., Moodie, C. A., Isik, A. I., Erramuzpe, A., Kent, J. D., Goncalves, M., DuPre, E., Snyder, M., Oya, H., Ghosh, S. S., Wright, J., Durnez, J., Poldrack, R. A., & Gorgolewski, K. J. (2019). fMRIPrep: a robust preprocessing pipeline for functional MRI. //Nature Methods//. [[https:~~/~~/doi.org/10.1038/s41592-018-0235-4>>https://doi.org/10.1038/s41592-018-0235-4]]
103 -
104 -
105 -Schirner, M., Rothmeier, S., Jirsa, V. K., McIntosh, A. R., & Ritter, P. (2015). An automated pipeline for constructing personalized virtual brains from multimodal neuroimaging data. NeuroImage, 117, 343-357.  
106 -
107 -
108 -Smith, R., & Connelly, A. (2019). MRtrix3_connectome: A BIDS Application for quantitative structural connectome construction. //OHBM//, W610.
109 -
110 -
111 -Tournier, J. D., Smith, R., Raffelt, D., Tabbara, R., Dhollander, T., Pietsch, M., Christiaens, D., Jeurissen, B., Yeh, C. H., & Connelly, A. (2019). MRtrix3: A fast, flexible and open software framework for medical image processing and visualisation. In //NeuroImage//. https:~/~/doi.org/10.1016/j.neuroimage.2019.116137
112 -)))
113 -
114 -== ==
115 -
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118 118  {{box title="**Contents**"}}
Collaboratory.Apps.Collab.Code.CollabClass[0]
Description
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1 -TVB Image Processing Pipeline With MINDS annotated Outputs
1 +Construct brain network models from empirical MRI data.
Public

TVB PIPELINE