Changes for page TVB PIPELINE

Last modified by ldomide on 2024/05/20 08:56
From version 40.1
edited by michaels
on 2021/11/30 10:56
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To version 45.1
edited by michaels
on 2023/05/22 10:12
Change comment: There is no comment for this version

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4 4  (((
5 5  == TVB Image Processing Pipeline ==
6 6  
7 -=== [[Web-GUI to configure and start processing on HPC>>https://thevirtualbrain.apps.hbp.eu/||target="_blank"]] ===
7 +=== [[Web-GUI to configure and start processing on HPC>>https://thevirtualbrain.apps.hbp.eu/||rel="noopener noreferrer" target="_blank"]] ===
8 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||rel="noopener noreferrer" target="_blank"]] ====
11 +==== [[Direct link to notebook>>https://drive.ebrains.eu/d/5e2fbc74575c47e88780/||rel="noopener noreferrer" target="_blank"]] ====
12 12  
13 13  [[image:8677353.png||style="float:left"]]
14 14  
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22 22  (((
23 23  == Quick links ==
24 24  
25 +* [[TVB Pipeline Web GUI>>https://thevirtualbrain.apps.hbp.eu/]]
25 25  * [[TVB on EBRAINS (Short Version)>>https://www.youtube.com/watch?v=EETRdGskiWQ&t=2s||rel="noopener noreferrer" target="_blank"]]
26 26  * [[TVB on EBRAINS (Long Version)>>https://www.youtube.com/watch?v=VYhR9RNRIpA&t=2s||rel="noopener noreferrer" target="_blank"]]
27 27  * [[TVB on EBRAINS (Mini Videos)>>url:https://www.youtube.com/playlist?list=PLVtblERyzDeLcVv4BbW3BvmO8D-qVZxKf||rel="noopener noreferrer" target="_blank"]]
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29 29  
30 30  == What can I find here? ==
31 31  
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
32 32  * an IPython notebook that describes how to
33 33  ** use the TVB processing pipeline on one of the associated supercomputers using PyUnicore
34 34  ** upload MRI data to the supercomputer
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48 48  == How do I use it? ==
49 49  
50 50  * the pipeline is implemented by three Docker containers (mrtrix3_connectome, fmriprep and tvb_converter)
51 -* the containers are executed on supercomputers and operated via the [[web GUI>>https://thevirtualbrain.apps.hbp.eu/]] or 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
52 52  * Find the notebook by clicking on "Drive" in the left menu. The notebook is located in the folder "notebooks"
53 -* 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]]
56 +* Direct link to notebook: [[https:~~/~~/drive.ebrains.eu/d/5e2fbc74575c47e88780/>>https://drive.ebrains.eu/d/5e2fbc74575c47e88780/]]
54 54  * To use the notebook, download it onto your local filesystem, create a new Collab and upload it there.
55 55  * Then, head over to [[https:~~/~~/lab.ebrains.eu/>>url:https://lab.ebrains.eu/||rel="noopener noreferrer" target="_blank"]] to edit and run your notebook.
56 56  * 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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105 105  == Citing this work ==
106 106  
107 107  
108 -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).
111 +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).
109 109  
110 110  
111 111  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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114 114  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.  
115 115  
116 116  
120 +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]]
121 +
122 +
117 117  Smith, R., & Connelly, A. (2019). MRtrix3_connectome: A BIDS Application for quantitative structural connectome construction. //OHBM//, W610.
118 118  
119 119  
Collaboratory.Apps.Collab.Code.CollabClass[0]
owner
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1 +michaels
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TVB PIPELINE