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
Change comment: There is no comment for this version
To version 47.1
edited by ldomide
on 2024/05/20 08:56
Change comment: There is no comment for this version

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2 2  (((
3 3  (% class="container" %)
4 4  (((
5 -= TVB Image Processing Pipeline With MINDS annotated Outputs =
5 +== TVB Image Processing Pipeline ==
6 6  
7 -== [[Pipeline Video Tutorial>>https://drive.google.com/file/d/1VcXf3GX3KoihF4UzJQXzuGL4XWoqj5Jr/view||rel="noopener noreferrer" target="_blank"]] ==
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"]] ==
9 +==== [[Direct link to notebook>>https://drive.ebrains.eu/d/5e2fbc74575c47e88780/||rel="noopener noreferrer" target="_blank"]] ====
10 10  
11 11  [[image:8677353.png||style="float:left"]]
12 12  
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18 18  (((
19 19  (% class="col-xs-12 col-sm-8" %)
20 20  (((
21 +== Quick links ==
22 +
23 +* [[TVB on EBRAINS (Short Version)>>https://www.youtube.com/watch?v=EETRdGskiWQ&t=2s||rel="noopener noreferrer" target="_blank"]]
24 +* [[TVB on EBRAINS (Long Version)>>https://www.youtube.com/watch?v=VYhR9RNRIpA&t=2s||rel="noopener noreferrer" target="_blank"]]
25 +* [[TVB on EBRAINS (Mini Videos)>>url:https://www.youtube.com/playlist?list=PLVtblERyzDeLcVv4BbW3BvmO8D-qVZxKf||rel="noopener noreferrer" target="_blank"]]
26 +* [[User Story>>url:https://wiki.ebrains.eu/bin/view/Collabs/user-story-tvb/]]
27 +
21 21  == What can I find here? ==
22 22  
30 +* the code underlying the pipeline including the orchestrator that manages processing on the supercomputer
23 23  * an IPython notebook that describes how to
24 24  ** use the TVB processing pipeline on one of the associated supercomputers using PyUnicore
25 25  ** upload MRI data to the supercomputer
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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)
42 -* the containers are executed on supercomputers and operated via IPython notebooks
50 +* the containers can be executed on supercomputers and operated via IPython notebooks
43 43  * Find the notebook by clicking on "Drive" in the left menu. The notebook is located in the folder "notebooks"
44 -* 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]]
52 +* Direct link to notebook: [[https:~~/~~/drive.ebrains.eu/d/5e2fbc74575c47e88780/>>https://drive.ebrains.eu/d/5e2fbc74575c47e88780/]]
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'"
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96 96  == Citing this work ==
97 97  
98 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).
107 +When using this pipeline for published work, please acknowledge Schirner et al. 2015, Schirner et al. 2022, MRtrix3, MRtrix3_connectome (R. Smith & Connelly, 2019; Tournier et al., 2019) and fmriprep (Esteban et al., 2019).
100 100  
101 101  
102 102  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]]
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105 105  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.  
106 106  
107 107  
116 +Schirner, Domide, Perdikis, Triebkorn, Stefanovski, Pai, Prodan, Valean, Palmer, Langford, Blickensdörfer, van der Vlag, Diaz-Pier, Peyser, Woodman, Zehl, Fousek, Petkoski, Kusch, Hashemi, Marinazzo, Mangin, Flöel, Akintoye, Stahl, Deco, McIntosh, Hilgetag, Morgan, Schuller, Upton, McMurtrie, Dickscheid, Bjaalie, Amunts, Mersmann, Jirsa, Ritter (2022). Brain Simulation as a Cloud Service: The Virtual Brain on the European Research Platform EBRAINS. //Neuroimage//. [[https:~~/~~/doi.org/10.1016/j.neuroimage.2022.118973>>https://doi.org/10.1016/j.neuroimage.2022.118973]]
117 +
118 +
108 108  Smith, R., & Connelly, A. (2019). MRtrix3_connectome: A BIDS Application for quantitative structural connectome construction. //OHBM//, W610.
109 109  
110 110  
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TVB PIPELINE