Changes for page TVB PIPELINE

Last modified by ldomide on 2024/05/20 08:56
From version 19.1
edited by michaels
on 2020/05/06 14:08
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To version 30.1
edited by michaels
on 2020/06/26 11:59
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2 2  (((
3 3  (% class="container" %)
4 4  (((
5 -= From MRI to Functional and Structural Connectivity =
5 += TVB Image Processing Pipeline With MINDS annotated Outputs =
6 6  
7 -Neuroimaging data preprocessing pipeline
8 -
9 9  == [[Pipeline Video Tutorial>>https://drive.google.com/file/d/1VcXf3GX3KoihF4UzJQXzuGL4XWoqj5Jr/view||rel="noopener noreferrer" target="_blank"]] ==
10 10  
9 +== [[Direct link to notebook>>https://drive.ebrains.eu/#my-libs/lib/42ac27a5-981e-4cf6-8ec5-d67b0c24bf09/notebooks||rel="noopener noreferrer" target="_blank"]] ==
11 11  
11 +
12 12  [[image:8677353.png||style="float:left"]]
13 13  
14 14  == ==
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36 36  == What can I find here? ==
37 37  
38 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
39 +** use the TVB processing pipeline on one of the associated supercomputers using PyUnicore
40 +** upload MRI data to the supercomputer
41 41  ** set up and run the pipeline
42 42  ** download processing results
43 43  
44 +== What does the TVB processing pipeline do? ==
45 +
46 +After uploading MRI data to the supercomputer, the pipeline runs the three containers
47 +
48 +* [[bids/mrtrix3_connectome>>https://hub.docker.com/r/bids/mrtrix3_connectome||rel="noopener noreferrer" target="_blank"]]
49 +* [[poldracklab/fmriprep>>https://hub.docker.com/r/poldracklab/fmriprep||rel="noopener noreferrer" target="_blank"]], and
50 +* [[thevirtualbrain/tvb_converter>>https://hub.docker.com/r/thevirtualbrain/tvb_converter||rel="noopener noreferrer" target="_blank"]]
51 +
52 +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.
53 +
44 44  == How do I use it? ==
45 45  
46 46  * the pipeline is implemented by three Docker containers (mrtrix3_connectome, fmriprep and tvb_converter)
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53 53  
54 54  == Metadata ==
55 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
66 +|=Category|tool
67 +|=Tags|(((
68 +* [[Simulaton>>url:https://services.humanbrainproject.eu/software-catalog/catalog/?ctx=97d59245-adce-42c4-8b50-d22587071fcd&ctxstate=search%2Ctvb]]
69 +* [[TVB>>url:https://services.humanbrainproject.eu/software-catalog/catalog/?ctx=97d59245-adce-42c4-8b50-d22587071fcd&ctxstate=search%2Ctvb]]
70 +* [[visualization>>url:https://services.humanbrainproject.eu/software-catalog/catalog/?ctx=97d59245-adce-42c4-8b50-d22587071fcd&ctxstate=search%2Ctvb]]
71 +* [[open-source>>url:https://services.humanbrainproject.eu/software-catalog/catalog/?ctx=97d59245-adce-42c4-8b50-d22587071fcd&ctxstate=search%2Ctvb]]
72 +* [[analysis>>url:https://services.humanbrainproject.eu/software-catalog/catalog/?ctx=97d59245-adce-42c4-8b50-d22587071fcd&ctxstate=search%2Ctvb]]
73 +* [[supercomputers>>url:https://services.humanbrainproject.eu/software-catalog/catalog/?ctx=97d59245-adce-42c4-8b50-d22587071fcd&ctxstate=search%2Ctvb]]
74 +* [[brain-model>>url:https://services.humanbrainproject.eu/software-catalog/catalog/?ctx=97d59245-adce-42c4-8b50-d22587071fcd&ctxstate=search%2Ctvb]]
75 +* [[neuroinformatics>>url:https://services.humanbrainproject.eu/software-catalog/catalog/?ctx=97d59245-adce-42c4-8b50-d22587071fcd&ctxstate=search%2Ctvb]]
76 +* [[image-segmentation>>url:https://services.humanbrainproject.eu/software-catalog/catalog/?ctx=97d59245-adce-42c4-8b50-d22587071fcd&ctxstate=search%2Ctvb]]
77 +* [[simulation>>url:https://services.humanbrainproject.eu/software-catalog/catalog/?ctx=97d59245-adce-42c4-8b50-d22587071fcd&ctxstate=search%2Ctvb]]
78 +* [[The-Virtual-Brain>>url:https://services.humanbrainproject.eu/software-catalog/catalog/?ctx=97d59245-adce-42c4-8b50-d22587071fcd&ctxstate=search%2Ctvb]]
64 64  )))
80 +|=Partners|(((
81 +* Charité Universitätsmedizin Berlin [[CHARITE>>url:https://services.humanbrainproject.eu/software-catalog/catalog/?ctx=97d59245-adce-42c4-8b50-d22587071fcd&ctxstate=search%2Ctvb]]
82 +)))
83 +|=Maintainers|(((
84 +* [[Petra Ritter>>path:mailto:petra.ritter@charite.de]]
85 +* [[Michael Schirner>>path:mailto:michael.schirner@charite.de]]
86 +* [[Paul Triebkorn>>path:mailto:jan-paul.triebkorn@charite.de]]
87 +)))
88 +|=Contributors|(((
89 +* [[Petra Ritter>>path:mailto:petra.ritter@charite.de]]
90 +* [[Michael Schirner>>path:mailto:michael.schirner@charite.de]]
91 +* [[Paul Triebkorn>>path:mailto:jan-paul.triebkorn@charite.de]]
92 +)))
93 +|=Homepage|[[https:~~/~~/www.brainsimulation.org>>url:https://www.brainsimulation.org/]]
94 +|=Documentation|[[https:~~/~~/drive.google.com/file/d/1VcXf3GX3KoihF4UzJQXzuGL4XWoqj5Jr/view>>url:https://drive.google.com/file/d/1VcXf3GX3KoihF4UzJQXzuGL4XWoqj5Jr/view]]
95 +|=Support|[[petra.ritter@charite.de>>path:mailto:petra.ritter@charite.de]]
96 +|=Source Code|[[https:~~/~~/hub.docker.com/r/thevirtualbrain/tvb_converter>>url:https://hub.docker.com/r/thevirtualbrain/tvb_converter]]
97 +|=Download Page|[[https:~~/~~/hub.docker.com/r/thevirtualbrain/tvb_converter>>url:https://hub.docker.com/r/thevirtualbrain/tvb_converter]]
98 +|=License|GPLv3
99 +|=Current Version|1.0
100 +|=All Versions|(((
101 +* 1.0
102 +)))
65 65  
104 +=== ===
66 66  
106 +== Publications on TVB/brain model preprocessing ==
107 +
108 +* [[https:~~/~~/www.ncbi.nlm.nih.gov/pubmed/25837600>>url:https://www.ncbi.nlm.nih.gov/pubmed/25837600]]
109 +* [[https:~~/~~/www.ncbi.nlm.nih.gov/pubmed/27480624>>url:https://www.ncbi.nlm.nih.gov/pubmed/27480624]]
110 +
111 +== Citing this work ==
112 +
113 +
114 +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).
115 +
116 +
117 +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]]
118 +
119 +
120 +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.  
121 +
122 +
123 +Smith, R., & Connelly, A. (2019). MRtrix3_connectome: A BIDS Application for quantitative structural connectome construction. //OHBM//, W610.
124 +
125 +
126 +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
127 +)))
128 +
129 +== ==
130 +
67 67  (% class="col-xs-12 col-sm-4" %)
68 68  (((
69 69  {{box title="**Contents**"}}
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TVB PIPELINE