Changes for page TVB PIPELINE

Last modified by ldomide on 2024/05/20 08:56
From version 21.1
edited by michaels
on 2020/05/06 14:12
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To version 41.1
edited by michaels
on 2021/11/30 10:58
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2 2  (((
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5 -= From MRI to Functional and Structural Connectivity =
5 +== TVB Image Processing Pipeline ==
6 6  
7 -Neuroimaging data preprocessing pipeline
7 +=== [[Web-GUI to configure and start processing on HPC>>https://thevirtualbrain.apps.hbp.eu/||rel="noopener noreferrer" target="_blank"]] ===
8 8  
9 -== [[Pipeline Video Tutorial>>https://drive.google.com/file/d/1VcXf3GX3KoihF4UzJQXzuGL4XWoqj5Jr/view||rel="noopener noreferrer" target="_blank"]] ==
9 +==== [[Pipeline Video Tutorial>>https://drive.google.com/file/d/1VcXf3GX3KoihF4UzJQXzuGL4XWoqj5Jr/view||rel="noopener noreferrer" target="_blank"]] ====
10 10  
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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23 +== Quick links ==
24 +
25 +* [[TVB Pipeline Web GUI>>https://thevirtualbrain.apps.hbp.eu/]]
26 +* [[TVB on EBRAINS (Short Version)>>https://www.youtube.com/watch?v=EETRdGskiWQ&t=2s||rel="noopener noreferrer" target="_blank"]]
27 +* [[TVB on EBRAINS (Long Version)>>https://www.youtube.com/watch?v=VYhR9RNRIpA&t=2s||rel="noopener noreferrer" target="_blank"]]
28 +* [[TVB on EBRAINS (Mini Videos)>>url:https://www.youtube.com/playlist?list=PLVtblERyzDeLcVv4BbW3BvmO8D-qVZxKf||rel="noopener noreferrer" target="_blank"]]
29 +* [[User Story>>url:https://wiki.ebrains.eu/bin/view/Collabs/user-story-tvb/]]
30 +
36 36  == What can I find here? ==
37 37  
33 +* a [[link>>https://thevirtualbrain.apps.hbp.eu/]] to the Web App for using the pipeline via GUI
34 +* the code underlying the pipeline including the orchestrator that manages processing on the supercomputer
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
36 +** use the TVB processing pipeline on one of the associated supercomputers using PyUnicore
37 +** upload MRI data to the supercomputer
41 41  ** set up and run the pipeline
42 42  ** download processing results
43 43  
41 +== What does the TVB processing pipeline do? ==
42 +
43 +After uploading MRI data to the supercomputer, the pipeline runs the three containers
44 +
45 +* [[bids/mrtrix3_connectome>>https://hub.docker.com/r/bids/mrtrix3_connectome||rel="noopener noreferrer" target="_blank"]]
46 +* [[poldracklab/fmriprep>>https://hub.docker.com/r/poldracklab/fmriprep||rel="noopener noreferrer" target="_blank"]], and
47 +* [[thevirtualbrain/tvb_converter>>https://hub.docker.com/r/thevirtualbrain/tvb_converter||rel="noopener noreferrer" target="_blank"]]
48 +
49 +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.
50 +
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)
47 -* the containers are executed on supercomputers and operated via IPython notebooks
54 +* the containers are executed on supercomputers and operated via the [[web GUI>>https://thevirtualbrain.apps.hbp.eu/]] or via IPython notebooks
48 48  * Find the notebook by clicking on "Drive" in the left menu. The notebook is located in the folder "notebooks"
49 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]]
50 50  * To use the notebook, download it onto your local filesystem, create a new Collab and upload it there.
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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
63 +|=Category|tool
64 +|=Tags|(((
65 +* [[Simulaton>>url:https://services.humanbrainproject.eu/software-catalog/catalog/?ctx=97d59245-adce-42c4-8b50-d22587071fcd&ctxstate=search%2Ctvb]]
66 +* [[TVB>>url:https://services.humanbrainproject.eu/software-catalog/catalog/?ctx=97d59245-adce-42c4-8b50-d22587071fcd&ctxstate=search%2Ctvb]]
67 +* [[visualization>>url:https://services.humanbrainproject.eu/software-catalog/catalog/?ctx=97d59245-adce-42c4-8b50-d22587071fcd&ctxstate=search%2Ctvb]]
68 +* [[open-source>>url:https://services.humanbrainproject.eu/software-catalog/catalog/?ctx=97d59245-adce-42c4-8b50-d22587071fcd&ctxstate=search%2Ctvb]]
69 +* [[analysis>>url:https://services.humanbrainproject.eu/software-catalog/catalog/?ctx=97d59245-adce-42c4-8b50-d22587071fcd&ctxstate=search%2Ctvb]]
70 +* [[supercomputers>>url:https://services.humanbrainproject.eu/software-catalog/catalog/?ctx=97d59245-adce-42c4-8b50-d22587071fcd&ctxstate=search%2Ctvb]]
71 +* [[brain-model>>url:https://services.humanbrainproject.eu/software-catalog/catalog/?ctx=97d59245-adce-42c4-8b50-d22587071fcd&ctxstate=search%2Ctvb]]
72 +* [[neuroinformatics>>url:https://services.humanbrainproject.eu/software-catalog/catalog/?ctx=97d59245-adce-42c4-8b50-d22587071fcd&ctxstate=search%2Ctvb]]
73 +* [[image-segmentation>>url:https://services.humanbrainproject.eu/software-catalog/catalog/?ctx=97d59245-adce-42c4-8b50-d22587071fcd&ctxstate=search%2Ctvb]]
74 +* [[simulation>>url:https://services.humanbrainproject.eu/software-catalog/catalog/?ctx=97d59245-adce-42c4-8b50-d22587071fcd&ctxstate=search%2Ctvb]]
75 +* [[The-Virtual-Brain>>url:https://services.humanbrainproject.eu/software-catalog/catalog/?ctx=97d59245-adce-42c4-8b50-d22587071fcd&ctxstate=search%2Ctvb]]
76 +)))
77 +|=Partners|(((
78 +* Charité Universitätsmedizin Berlin [[CHARITE>>url:https://services.humanbrainproject.eu/software-catalog/catalog/?ctx=97d59245-adce-42c4-8b50-d22587071fcd&ctxstate=search%2Ctvb]]
79 +)))
80 +|=Maintainers|(((
81 +* [[Petra Ritter>>path:mailto:petra.ritter@charite.de]]
82 +* [[Michael Schirner>>path:mailto:michael.schirner@charite.de]]
83 +* [[Paul Triebkorn>>path:mailto:jan-paul.triebkorn@charite.de]]
84 +)))
85 +|=Contributors|(((
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 +|=Homepage|[[https:~~/~~/www.brainsimulation.org>>url:https://www.brainsimulation.org/]]
91 +|=Documentation|[[https:~~/~~/drive.google.com/file/d/1VcXf3GX3KoihF4UzJQXzuGL4XWoqj5Jr/view>>url:https://drive.google.com/file/d/1VcXf3GX3KoihF4UzJQXzuGL4XWoqj5Jr/view]]
92 +|=Support|[[petra.ritter@charite.de>>path:mailto:petra.ritter@charite.de]]
93 +|=Source Code|[[https:~~/~~/hub.docker.com/r/thevirtualbrain/tvb_converter>>url:https://hub.docker.com/r/thevirtualbrain/tvb_converter]]
94 +|=Download Page|[[https:~~/~~/hub.docker.com/r/thevirtualbrain/tvb_converter>>url:https://hub.docker.com/r/thevirtualbrain/tvb_converter]]
95 +|=License|GPLv3
96 +|=Current Version|1.0
97 +|=All Versions|(((
98 +* 1.0
99 +)))
64 64  
101 +=== ===
102 +
65 65  == Publications on TVB/brain model preprocessing ==
66 66  
67 67  * [[https:~~/~~/www.ncbi.nlm.nih.gov/pubmed/25837600>>url:https://www.ncbi.nlm.nih.gov/pubmed/25837600]]
68 68  * [[https:~~/~~/www.ncbi.nlm.nih.gov/pubmed/27480624>>url:https://www.ncbi.nlm.nih.gov/pubmed/27480624]]
107 +
108 +== Citing this work ==
109 +
110 +
111 +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).
112 +
113 +
114 +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]]
115 +
116 +
117 +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.  
118 +
119 +
120 +Smith, R., & Connelly, A. (2019). MRtrix3_connectome: A BIDS Application for quantitative structural connectome construction. //OHBM//, W610.
121 +
122 +
123 +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
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1 -Construct brain network models from empirical MRI data.
1 +TVB Image Processing Pipeline With MINDS annotated Outputs
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TVB PIPELINE