Changes for page TVB PIPELINE

Last modified by ldomide on 2024/05/20 08:56
From version 46.1
edited by ldomide
on 2024/04/08 13:45
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To version 27.1
edited by michaels
on 2020/06/12 10:43
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1 -XWiki.ldomide
1 +XWiki.michaels
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2 2  (((
3 3  (% class="container" %)
4 4  (((
5 -== TVB Image Processing Pipeline ==
5 += From MRI to Functional and Structural Connectivity =
6 6  
7 -==== [[Pipeline Video Tutorial>>https://drive.google.com/file/d/1VcXf3GX3KoihF4UzJQXzuGL4XWoqj5Jr/view||rel="noopener noreferrer" target="_blank"]] ====
7 +Neuroimaging data preprocessing pipeline
8 8  
9 -==== [[Direct link to notebook>>https://drive.ebrains.eu/d/5e2fbc74575c47e88780/||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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11 11  [[image:8677353.png||style="float:left"]]
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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 -
28 28  == What can I find here? ==
29 29  
30 -* the code underlying the pipeline including the orchestrator that manages processing on the supercomputer
31 31  * an IPython notebook that describes how to
32 32  ** use the TVB processing pipeline on one of the associated supercomputers using PyUnicore
33 33  ** upload MRI data to the supercomputer
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47 47  == How do I use it? ==
48 48  
49 49  * the pipeline is implemented by three Docker containers (mrtrix3_connectome, fmriprep and tvb_converter)
50 -* the containers are executed on supercomputers and operated via the [[web GUI>>https://thevirtualbrain.apps.hbp.eu/]] or via IPython notebooks
59 +* the containers are executed on supercomputers and operated via IPython notebooks
51 51  * Find the notebook by clicking on "Drive" in the left menu. The notebook is located in the folder "notebooks"
52 -* Direct link to notebook: [[https:~~/~~/drive.ebrains.eu/d/5e2fbc74575c47e88780/>>https://drive.ebrains.eu/d/5e2fbc74575c47e88780/]]
61 +* 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]]
53 53  * To use the notebook, download it onto your local filesystem, create a new Collab and upload it there.
54 54  * Then, head over to [[https:~~/~~/lab.ebrains.eu/>>url:https://lab.ebrains.eu/||rel="noopener noreferrer" target="_blank"]] to edit and run your notebook.
55 55  * 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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104 104  == Citing this work ==
105 105  
106 106  
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).
116 +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).
108 108  
109 109  
110 -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]]
119 +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
111 111  
112 112  
113 -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.  
114 -
115 -
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 -
119 119  Smith, R., & Connelly, A. (2019). MRtrix3_connectome: A BIDS Application for quantitative structural connectome construction. //OHBM//, W610.
120 120  
121 121  
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1 -TVB Image Processing Pipeline With MINDS annotated Outputs
1 +Construct brain network models from empirical MRI data.
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TVB PIPELINE