Wiki source code of TVB PIPELINE

Version 44.1 by petritter on 2023/04/30 14:34

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40.1	5	== TVB Image Processing Pipeline ==
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41.1	7	=== [[Web-GUI to configure and start processing on HPC>>https://thevirtualbrain.apps.hbp.eu/\|\|rel="noopener noreferrer" target="_blank"]] ===
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40.1	9	==== [[Pipeline Video Tutorial>>https://drive.google.com/file/d/1VcXf3GX3KoihF4UzJQXzuGL4XWoqj5Jr/view\|\|rel="noopener noreferrer" target="_blank"]] ====
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40.1	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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33.1	23	== Quick links ==
	24
41.1	25	* [[TVB Pipeline Web GUI>>https://thevirtualbrain.apps.hbp.eu/]]
37.1	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"]]
33.1	29	* [[User Story>>url:https://wiki.ebrains.eu/bin/view/Collabs/user-story-tvb/]]
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8.1	31	== What can I find here? ==
1.1	32
41.1	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
7.1	35	* an IPython notebook that describes how to
25.1	36	** use the TVB processing pipeline on one of the associated supercomputers using PyUnicore
	37	** upload MRI data to the supercomputer
7.1	38	** set up and run the pipeline
	39	** download processing results
8.1	40
25.1	41	== What does the TVB processing pipeline do? ==
	42
	43	After uploading MRI data to the supercomputer, the pipeline runs the three containers
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26.1	45	* [[bids/mrtrix3_connectome>>https://hub.docker.com/r/bids/mrtrix3_connectome\|\|rel="noopener noreferrer" target="_blank"]]
	46	* [[poldracklab/fmriprep>>https://hub.docker.com/r/poldracklab/fmriprep\|\|rel="noopener noreferrer" target="_blank"]], and
	47	* [[thevirtualbrain/tvb_converter>>https://hub.docker.com/r/thevirtualbrain/tvb_converter\|\|rel="noopener noreferrer" target="_blank"]]
25.1	48
	49	The TVB Processing Pipeline takes multimodal MRI data sets (anatomical, functional and diffusion-weighted MRI) as input and generates SCs, region-average fMRI time series, FCs, brain surfaces, electrode positions, lead field matrices, and atlas parcellations as output. The pipeline performs preprocessing and distortion-correction on MRI data as well as white matter fiber bundle tractography on diffusion data. Outputs are formatted according to two data standards: a TVB-ready data set that can be directly used to simulate brain network models and the same output in BIDS format.
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8.1	51	== How do I use it? ==
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	53	* the pipeline is implemented by three Docker containers (mrtrix3_connectome, fmriprep and tvb_converter)
41.1	54	* the containers are executed on supercomputers and operated via the [[web GUI>>https://thevirtualbrain.apps.hbp.eu/]] or via IPython notebooks
8.1	55	* Find the notebook by clicking on "Drive" in the left menu. The notebook is located in the folder "notebooks"
10.1	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]]
8.1	57	* To use the notebook, download it onto your local filesystem, create a new Collab and upload it there.
10.1	58	* Then, head over to [[https:~~/~~/lab.ebrains.eu/>>url:https://lab.ebrains.eu/\|\|rel="noopener noreferrer" target="_blank"]] to edit and run your notebook.
8.1	59	* 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'"
19.1	60
	61	== Metadata ==
	62
23.1	63	\|=Category\|tool
	64	\|=Tags\|(((
	65	* [[Simulaton>>url:https://services.humanbrainproject.eu/software-catalog/catalog/?ctx=97d59245-adce-42c4-8b50-d22587071fcd&ctxstate=search%2Ctvb]]
	66	* [[TVB>>url:https://services.humanbrainproject.eu/software-catalog/catalog/?ctx=97d59245-adce-42c4-8b50-d22587071fcd&ctxstate=search%2Ctvb]]
	67	* [[visualization>>url:https://services.humanbrainproject.eu/software-catalog/catalog/?ctx=97d59245-adce-42c4-8b50-d22587071fcd&ctxstate=search%2Ctvb]]
	68	* [[open-source>>url:https://services.humanbrainproject.eu/software-catalog/catalog/?ctx=97d59245-adce-42c4-8b50-d22587071fcd&ctxstate=search%2Ctvb]]
	69	* [[analysis>>url:https://services.humanbrainproject.eu/software-catalog/catalog/?ctx=97d59245-adce-42c4-8b50-d22587071fcd&ctxstate=search%2Ctvb]]
	70	* [[supercomputers>>url:https://services.humanbrainproject.eu/software-catalog/catalog/?ctx=97d59245-adce-42c4-8b50-d22587071fcd&ctxstate=search%2Ctvb]]
	71	* [[brain-model>>url:https://services.humanbrainproject.eu/software-catalog/catalog/?ctx=97d59245-adce-42c4-8b50-d22587071fcd&ctxstate=search%2Ctvb]]
	72	* [[neuroinformatics>>url:https://services.humanbrainproject.eu/software-catalog/catalog/?ctx=97d59245-adce-42c4-8b50-d22587071fcd&ctxstate=search%2Ctvb]]
	73	* [[image-segmentation>>url:https://services.humanbrainproject.eu/software-catalog/catalog/?ctx=97d59245-adce-42c4-8b50-d22587071fcd&ctxstate=search%2Ctvb]]
	74	* [[simulation>>url:https://services.humanbrainproject.eu/software-catalog/catalog/?ctx=97d59245-adce-42c4-8b50-d22587071fcd&ctxstate=search%2Ctvb]]
	75	* [[The-Virtual-Brain>>url:https://services.humanbrainproject.eu/software-catalog/catalog/?ctx=97d59245-adce-42c4-8b50-d22587071fcd&ctxstate=search%2Ctvb]]
	76	)))
	77	\|=Partners\|(((
	78	* Charité Universitätsmedizin Berlin [[CHARITE>>url:https://services.humanbrainproject.eu/software-catalog/catalog/?ctx=97d59245-adce-42c4-8b50-d22587071fcd&ctxstate=search%2Ctvb]]
	79	)))
	80	\|=Maintainers\|(((
	81	* [[Petra Ritter>>path:mailto:petra.ritter@charite.de]]
	82	* [[Michael Schirner>>path:mailto:michael.schirner@charite.de]]
	83	* [[Paul Triebkorn>>path:mailto:jan-paul.triebkorn@charite.de]]
	84	)))
	85	\|=Contributors\|(((
	86	* [[Petra Ritter>>path:mailto:petra.ritter@charite.de]]
	87	* [[Michael Schirner>>path:mailto:michael.schirner@charite.de]]
	88	* [[Paul Triebkorn>>path:mailto:jan-paul.triebkorn@charite.de]]
	89	)))
	90	\|=Homepage\|[[https:~~/~~/www.brainsimulation.org>>url:https://www.brainsimulation.org/]]
	91	\|=Documentation\|[[https:~~/~~/drive.google.com/file/d/1VcXf3GX3KoihF4UzJQXzuGL4XWoqj5Jr/view>>url:https://drive.google.com/file/d/1VcXf3GX3KoihF4UzJQXzuGL4XWoqj5Jr/view]]
	92	\|=Support\|[[petra.ritter@charite.de>>path:mailto:petra.ritter@charite.de]]
	93	\|=Source Code\|[[https:~~/~~/hub.docker.com/r/thevirtualbrain/tvb_converter>>url:https://hub.docker.com/r/thevirtualbrain/tvb_converter]]
	94	\|=Download Page\|[[https:~~/~~/hub.docker.com/r/thevirtualbrain/tvb_converter>>url:https://hub.docker.com/r/thevirtualbrain/tvb_converter]]
	95	\|=License\|GPLv3
	96	\|=Current Version\|1.0
	97	\|=All Versions\|(((
	98	* 1.0
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20.1	100
24.1	101	=== ===
23.1	102
21.1	103	== Publications on TVB/brain model preprocessing ==
20.1	104
	105	* [[https:~~/~~/www.ncbi.nlm.nih.gov/pubmed/25837600>>url:https://www.ncbi.nlm.nih.gov/pubmed/25837600]]
	106	* [[https:~~/~~/www.ncbi.nlm.nih.gov/pubmed/27480624>>url:https://www.ncbi.nlm.nih.gov/pubmed/27480624]]
26.1	107
	108	== Citing this work ==
	109
	110
44.1	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).
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28.1	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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29.1	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.
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44.1	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]]
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	122
26.1	123	Smith, R., & Connelly, A. (2019). MRtrix3_connectome: A BIDS Application for quantitative structural connectome construction. //OHBM//, W610.
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	126	Tournier, J. D., Smith, R., Raffelt, D., Tabbara, R., Dhollander, T., Pietsch, M., Christiaens, D., Jeurissen, B., Yeh, C. H., & Connelly, A. (2019). MRtrix3: A fast, flexible and open software framework for medical image processing and visualisation. In //NeuroImage//. https:~/~/doi.org/10.1016/j.neuroimage.2019.116137
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26.1	129	== ==
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	133	{{box title="Contents"}}
	134	{{toc/}}
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