Changes for page TVB PIPELINE

Last modified by ldomide on 2024/05/20 08:56
From version 17.1
edited by michaels
on 2020/05/06 13:44
Change comment: There is no comment for this version
To version 32.1
edited by michaels
on 2020/06/26 12:24
Change comment: There is no comment for this version

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2 2  (((
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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
7 +== [[Pipeline Video Tutorial>>https://drive.google.com/file/d/1VcXf3GX3KoihF4UzJQXzuGL4XWoqj5Jr/view||rel="noopener noreferrer" target="_blank"]] ==
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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34 -== [[Pipeline Video Tutorial>>https://drive.google.com/file/d/1VcXf3GX3KoihF4UzJQXzuGL4XWoqj5Jr/view||rel="noopener noreferrer" target="_blank"]] ==
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36 36  )))
37 37  
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42 42  == What can I find here? ==
43 43  
44 44  * an IPython notebook that describes how to
45 -** use the TVB pipeline on one of the associated supercomputers using PyUnicore
46 -** upload model data to the supercomputer
24 +** use the TVB processing pipeline on one of the associated supercomputers using PyUnicore
25 +** upload MRI data to the supercomputer
47 47  ** set up and run the pipeline
48 48  ** download processing results
49 49  
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 +
50 50  == How do I use it? ==
51 51  
52 52  * the pipeline is implemented by three Docker containers (mrtrix3_connectome, fmriprep and tvb_converter)
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56 56  * To use the notebook, download it onto your local filesystem, create a new Collab and upload it there.
57 57  * Then, head over to [[https:~~/~~/lab.ebrains.eu/>>url:https://lab.ebrains.eu/||rel="noopener noreferrer" target="_blank"]] to edit and run your notebook.
58 58  * 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]]
59 59  )))
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 +)))
60 60  
89 +=== ===
61 61  
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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63 63  (((
64 64  {{box title="**Contents**"}}
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