Changes for page TVB PIPELINE

Last modified by ldomide on 2024/05/20 08:56
From version 42.1
edited by michaels
on 2022/03/22 18:10
Change comment: Migrated property [owner] from class [Collaboratory.Apps.Collab.Code.CollabClass]
To version 28.1
edited by michaels
on 2020/06/26 11:57
Change comment: There is no comment for this version

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2 2  (((
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5 -== TVB Image Processing Pipeline ==
5 += From MRI to Functional and Structural Connectivity =
6 6  
7 -=== [[Web-GUI to configure and start processing on HPC>>https://thevirtualbrain.apps.hbp.eu/||rel="noopener noreferrer" target="_blank"]] ===
7 +Neuroimaging data preprocessing pipeline
8 8  
9 -==== [[Pipeline Video Tutorial>>https://drive.google.com/file/d/1VcXf3GX3KoihF4UzJQXzuGL4XWoqj5Jr/view||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"]] ====
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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23 -== Quick links ==
24 -
25 -* [[TVB Pipeline Web GUI>>https://thevirtualbrain.apps.hbp.eu/]]
26 -* [[TVB on EBRAINS (Short Version)>>https://www.youtube.com/watch?v=EETRdGskiWQ&t=2s||rel="noopener noreferrer" target="_blank"]]
27 -* [[TVB on EBRAINS (Long Version)>>https://www.youtube.com/watch?v=VYhR9RNRIpA&t=2s||rel="noopener noreferrer" target="_blank"]]
28 -* [[TVB on EBRAINS (Mini Videos)>>url:https://www.youtube.com/playlist?list=PLVtblERyzDeLcVv4BbW3BvmO8D-qVZxKf||rel="noopener noreferrer" target="_blank"]]
29 -* [[User Story>>url:https://wiki.ebrains.eu/bin/view/Collabs/user-story-tvb/]]
30 -
31 31  == What can I find here? ==
32 32  
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
35 35  * an IPython notebook that describes how to
36 36  ** use the TVB processing pipeline on one of the associated supercomputers using PyUnicore
37 37  ** upload MRI data to the supercomputer
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51 51  == How do I use it? ==
52 52  
53 53  * the pipeline is implemented by three Docker containers (mrtrix3_connectome, fmriprep and tvb_converter)
54 -* 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
55 55  * Find the notebook by clicking on "Drive" in the left menu. The notebook is located in the folder "notebooks"
56 56  * 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]]
57 57  * To use the notebook, download it onto your local filesystem, create a new Collab and upload it there.
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114 114  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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116 116  
117 -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.  
122 +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. 
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125 +
120 120  Smith, R., & Connelly, A. (2019). MRtrix3_connectome: A BIDS Application for quantitative structural connectome construction. //OHBM//, W610.
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122 122  
Collaboratory.Apps.Collab.Code.CollabClass[0]
Description
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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