Changes for page TVB PIPELINE

Last modified by ldomide on 2024/05/20 08:56
From version 38.1
edited by michaels
on 2021/04/16 21:31
Change comment: There is no comment for this version
To version 46.1
edited by ldomide
on 2024/04/08 13:45
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 =
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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27 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
30 30  * an IPython notebook that describes how to
31 31  ** use the TVB processing pipeline on one of the associated supercomputers using PyUnicore
32 32  ** upload MRI data to the supercomputer
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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)
49 -* the containers are executed on supercomputers and operated via IPython notebooks
50 +* the containers are executed on supercomputers and operated via the [[web GUI>>https://thevirtualbrain.apps.hbp.eu/]] or via IPython notebooks
50 50  * Find the notebook by clicking on "Drive" in the left menu. The notebook is located in the folder "notebooks"
51 -* 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/]]
52 52  * To use the notebook, download it onto your local filesystem, create a new Collab and upload it there.
53 53  * Then, head over to [[https:~~/~~/lab.ebrains.eu/>>url:https://lab.ebrains.eu/||rel="noopener noreferrer" target="_blank"]] to edit and run your notebook.
54 54  * 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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103 103  == Citing this work ==
104 104  
105 105  
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 +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).
107 107  
108 108  
109 109  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]]
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112 112  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.  
113 113  
114 114  
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 +
115 115  Smith, R., & Connelly, A. (2019). MRtrix3_connectome: A BIDS Application for quantitative structural connectome construction. //OHBM//, W610.
116 116  
117 117  
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TVB PIPELINE