Changes for page TVB PIPELINE

Last modified by ldomide on 2024/05/20 08:56
From version 22.1
edited by michaels
on 2020/05/06 14:26
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To version 33.1
edited by michaels
on 2020/07/06 09:37
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2 2  (((
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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  
11 -== [[Direct link to notebook>>https://drive.ebrains.eu/#my-libs/lib/42ac27a5-981e-4cf6-8ec5-d67b0c24bf09/notebooks||target="_blank"]] ==
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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21 +== Quick links ==
22 +
23 +* [[TVB on EBRAINS (Short Version)>>url:https://www.youtube.com/watch?v=_G_DjRb1ams&feature=youtu.be]]
24 +* [[TVB on EBRAINS (Long Version)>>url:https://www.youtube.com/watch?v=eZrh6ztGFAY&feature=youtu.be]]
25 +* [[TVB on EBRAINS (Mini Videos)>>url:https://www.youtube.com/playlist?list=PLVtblERyzDeLcVv4BbW3BvmO8D-qVZxKf]]
26 +* [[User Story>>url:https://wiki.ebrains.eu/bin/view/Collabs/user-story-tvb/]]
27 +
38 38  == What can I find here? ==
39 39  
40 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
31 +** use the TVB processing pipeline on one of the associated supercomputers using PyUnicore
32 +** upload MRI data to the supercomputer
43 43  ** set up and run the pipeline
44 44  ** download processing results
45 45  
36 +== What does the TVB processing pipeline do? ==
37 +
38 +After uploading MRI data to the supercomputer, the pipeline runs the three containers
39 +
40 +* [[bids/mrtrix3_connectome>>https://hub.docker.com/r/bids/mrtrix3_connectome||rel="noopener noreferrer" target="_blank"]]
41 +* [[poldracklab/fmriprep>>https://hub.docker.com/r/poldracklab/fmriprep||rel="noopener noreferrer" target="_blank"]], and
42 +* [[thevirtualbrain/tvb_converter>>https://hub.docker.com/r/thevirtualbrain/tvb_converter||rel="noopener noreferrer" target="_blank"]]
43 +
44 +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.
45 +
46 46  == How do I use it? ==
47 47  
48 48  * the pipeline is implemented by three Docker containers (mrtrix3_connectome, fmriprep and tvb_converter)
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55 55  
56 56  == Metadata ==
57 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
58 +|=Category|tool
59 +|=Tags|(((
60 +* [[Simulaton>>url:https://services.humanbrainproject.eu/software-catalog/catalog/?ctx=97d59245-adce-42c4-8b50-d22587071fcd&ctxstate=search%2Ctvb]]
61 +* [[TVB>>url:https://services.humanbrainproject.eu/software-catalog/catalog/?ctx=97d59245-adce-42c4-8b50-d22587071fcd&ctxstate=search%2Ctvb]]
62 +* [[visualization>>url:https://services.humanbrainproject.eu/software-catalog/catalog/?ctx=97d59245-adce-42c4-8b50-d22587071fcd&ctxstate=search%2Ctvb]]
63 +* [[open-source>>url:https://services.humanbrainproject.eu/software-catalog/catalog/?ctx=97d59245-adce-42c4-8b50-d22587071fcd&ctxstate=search%2Ctvb]]
64 +* [[analysis>>url:https://services.humanbrainproject.eu/software-catalog/catalog/?ctx=97d59245-adce-42c4-8b50-d22587071fcd&ctxstate=search%2Ctvb]]
65 +* [[supercomputers>>url:https://services.humanbrainproject.eu/software-catalog/catalog/?ctx=97d59245-adce-42c4-8b50-d22587071fcd&ctxstate=search%2Ctvb]]
66 +* [[brain-model>>url:https://services.humanbrainproject.eu/software-catalog/catalog/?ctx=97d59245-adce-42c4-8b50-d22587071fcd&ctxstate=search%2Ctvb]]
67 +* [[neuroinformatics>>url:https://services.humanbrainproject.eu/software-catalog/catalog/?ctx=97d59245-adce-42c4-8b50-d22587071fcd&ctxstate=search%2Ctvb]]
68 +* [[image-segmentation>>url:https://services.humanbrainproject.eu/software-catalog/catalog/?ctx=97d59245-adce-42c4-8b50-d22587071fcd&ctxstate=search%2Ctvb]]
69 +* [[simulation>>url:https://services.humanbrainproject.eu/software-catalog/catalog/?ctx=97d59245-adce-42c4-8b50-d22587071fcd&ctxstate=search%2Ctvb]]
70 +* [[The-Virtual-Brain>>url:https://services.humanbrainproject.eu/software-catalog/catalog/?ctx=97d59245-adce-42c4-8b50-d22587071fcd&ctxstate=search%2Ctvb]]
71 +)))
72 +|=Partners|(((
73 +* Charité Universitätsmedizin Berlin [[CHARITE>>url:https://services.humanbrainproject.eu/software-catalog/catalog/?ctx=97d59245-adce-42c4-8b50-d22587071fcd&ctxstate=search%2Ctvb]]
74 +)))
75 +|=Maintainers|(((
76 +* [[Petra Ritter>>path:mailto:petra.ritter@charite.de]]
77 +* [[Michael Schirner>>path:mailto:michael.schirner@charite.de]]
78 +* [[Paul Triebkorn>>path:mailto:jan-paul.triebkorn@charite.de]]
79 +)))
80 +|=Contributors|(((
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 +|=Homepage|[[https:~~/~~/www.brainsimulation.org>>url:https://www.brainsimulation.org/]]
86 +|=Documentation|[[https:~~/~~/drive.google.com/file/d/1VcXf3GX3KoihF4UzJQXzuGL4XWoqj5Jr/view>>url:https://drive.google.com/file/d/1VcXf3GX3KoihF4UzJQXzuGL4XWoqj5Jr/view]]
87 +|=Support|[[petra.ritter@charite.de>>path:mailto:petra.ritter@charite.de]]
88 +|=Source Code|[[https:~~/~~/hub.docker.com/r/thevirtualbrain/tvb_converter>>url:https://hub.docker.com/r/thevirtualbrain/tvb_converter]]
89 +|=Download Page|[[https:~~/~~/hub.docker.com/r/thevirtualbrain/tvb_converter>>url:https://hub.docker.com/r/thevirtualbrain/tvb_converter]]
90 +|=License|GPLv3
91 +|=Current Version|1.0
92 +|=All Versions|(((
93 +* 1.0
94 +)))
66 66  
96 +=== ===
97 +
67 67  == Publications on TVB/brain model preprocessing ==
68 68  
69 69  * [[https:~~/~~/www.ncbi.nlm.nih.gov/pubmed/25837600>>url:https://www.ncbi.nlm.nih.gov/pubmed/25837600]]
70 70  * [[https:~~/~~/www.ncbi.nlm.nih.gov/pubmed/27480624>>url:https://www.ncbi.nlm.nih.gov/pubmed/27480624]]
102 +
103 +== Citing this work ==
104 +
105 +
106 +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).
107 +
108 +
109 +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]]
110 +
111 +
112 +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.  
113 +
114 +
115 +Smith, R., & Connelly, A. (2019). MRtrix3_connectome: A BIDS Application for quantitative structural connectome construction. //OHBM//, W610.
116 +
117 +
118 +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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121 +== ==
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Collaboratory.Apps.Collab.Code.CollabClass[0]
Description
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1 -Construct brain network models from empirical MRI data.
1 +TVB Image Processing Pipeline With MINDS annotated Outputs
Public

TVB PIPELINE