Wiki source code of TVB PIPELINE

Last modified by ldomide on 2024/05/20 08:56

version	line-number	content
1.1	1	(% class="jumbotron" %)
	2	(((
	3	(% class="container" %)
	4	(((
40.1	5	== TVB Image Processing Pipeline ==
1.1	6
40.1	7	==== [[Pipeline Video Tutorial>>https://drive.google.com/file/d/1VcXf3GX3KoihF4UzJQXzuGL4XWoqj5Jr/view\|\|rel="noopener noreferrer" target="_blank"]] ====
16.1	8
45.1	9	==== [[Direct link to notebook>>https://drive.ebrains.eu/d/5e2fbc74575c47e88780/\|\|rel="noopener noreferrer" target="_blank"]] ====
40.1	10
18.1	11	[[image:8677353.png\|\|style="float:left"]]
16.1	12
32.1	13
1.1	14	)))
	15	)))
	16
	17	(% class="row" %)
	18	(((
	19	(% class="col-xs-12 col-sm-8" %)
	20	(((
33.1	21	== Quick links ==
	22
37.1	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"]]
33.1	26	* [[User Story>>url:https://wiki.ebrains.eu/bin/view/Collabs/user-story-tvb/]]
	27
8.1	28	== What can I find here? ==
1.1	29
41.1	30	* the code underlying the pipeline including the orchestrator that manages processing on the supercomputer
7.1	31	* an IPython notebook that describes how to
25.1	32	** use the TVB processing pipeline on one of the associated supercomputers using PyUnicore
	33	** upload MRI data to the supercomputer
7.1	34	** set up and run the pipeline
	35	** download processing results
8.1	36
25.1	37	== What does the TVB processing pipeline do? ==
	38
	39	After uploading MRI data to the supercomputer, the pipeline runs the three containers
	40
26.1	41	* [[bids/mrtrix3_connectome>>https://hub.docker.com/r/bids/mrtrix3_connectome\|\|rel="noopener noreferrer" target="_blank"]]
	42	* [[poldracklab/fmriprep>>https://hub.docker.com/r/poldracklab/fmriprep\|\|rel="noopener noreferrer" target="_blank"]], and
	43	* [[thevirtualbrain/tvb_converter>>https://hub.docker.com/r/thevirtualbrain/tvb_converter\|\|rel="noopener noreferrer" target="_blank"]]
25.1	44
	45	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.
	46
8.1	47	== How do I use it? ==
	48
	49	* the pipeline is implemented by three Docker containers (mrtrix3_connectome, fmriprep and tvb_converter)
47.1	50	* the containers can be executed on supercomputers and operated via IPython notebooks
8.1	51	* Find the notebook by clicking on "Drive" in the left menu. The notebook is located in the folder "notebooks"
45.1	52	* Direct link to notebook: [[https:~~/~~/drive.ebrains.eu/d/5e2fbc74575c47e88780/>>https://drive.ebrains.eu/d/5e2fbc74575c47e88780/]]
8.1	53	* To use the notebook, download it onto your local filesystem, create a new Collab and upload it there.
10.1	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.
8.1	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'"
19.1	56
	57	== Metadata ==
	58
23.1	59	\|=Category\|tool
	60	\|=Tags\|(((
	61	* [[Simulaton>>url:https://services.humanbrainproject.eu/software-catalog/catalog/?ctx=97d59245-adce-42c4-8b50-d22587071fcd&ctxstate=search%2Ctvb]]
	62	* [[TVB>>url:https://services.humanbrainproject.eu/software-catalog/catalog/?ctx=97d59245-adce-42c4-8b50-d22587071fcd&ctxstate=search%2Ctvb]]
	63	* [[visualization>>url:https://services.humanbrainproject.eu/software-catalog/catalog/?ctx=97d59245-adce-42c4-8b50-d22587071fcd&ctxstate=search%2Ctvb]]
	64	* [[open-source>>url:https://services.humanbrainproject.eu/software-catalog/catalog/?ctx=97d59245-adce-42c4-8b50-d22587071fcd&ctxstate=search%2Ctvb]]
	65	* [[analysis>>url:https://services.humanbrainproject.eu/software-catalog/catalog/?ctx=97d59245-adce-42c4-8b50-d22587071fcd&ctxstate=search%2Ctvb]]
	66	* [[supercomputers>>url:https://services.humanbrainproject.eu/software-catalog/catalog/?ctx=97d59245-adce-42c4-8b50-d22587071fcd&ctxstate=search%2Ctvb]]
	67	* [[brain-model>>url:https://services.humanbrainproject.eu/software-catalog/catalog/?ctx=97d59245-adce-42c4-8b50-d22587071fcd&ctxstate=search%2Ctvb]]
	68	* [[neuroinformatics>>url:https://services.humanbrainproject.eu/software-catalog/catalog/?ctx=97d59245-adce-42c4-8b50-d22587071fcd&ctxstate=search%2Ctvb]]
	69	* [[image-segmentation>>url:https://services.humanbrainproject.eu/software-catalog/catalog/?ctx=97d59245-adce-42c4-8b50-d22587071fcd&ctxstate=search%2Ctvb]]
	70	* [[simulation>>url:https://services.humanbrainproject.eu/software-catalog/catalog/?ctx=97d59245-adce-42c4-8b50-d22587071fcd&ctxstate=search%2Ctvb]]
	71	* [[The-Virtual-Brain>>url:https://services.humanbrainproject.eu/software-catalog/catalog/?ctx=97d59245-adce-42c4-8b50-d22587071fcd&ctxstate=search%2Ctvb]]
	72	)))
	73	\|=Partners\|(((
	74	* Charité Universitätsmedizin Berlin [[CHARITE>>url:https://services.humanbrainproject.eu/software-catalog/catalog/?ctx=97d59245-adce-42c4-8b50-d22587071fcd&ctxstate=search%2Ctvb]]
	75	)))
	76	\|=Maintainers\|(((
	77	* [[Petra Ritter>>path:mailto:petra.ritter@charite.de]]
	78	* [[Michael Schirner>>path:mailto:michael.schirner@charite.de]]
	79	* [[Paul Triebkorn>>path:mailto:jan-paul.triebkorn@charite.de]]
	80	)))
	81	\|=Contributors\|(((
	82	* [[Petra Ritter>>path:mailto:petra.ritter@charite.de]]
	83	* [[Michael Schirner>>path:mailto:michael.schirner@charite.de]]
	84	* [[Paul Triebkorn>>path:mailto:jan-paul.triebkorn@charite.de]]
	85	)))
	86	\|=Homepage\|[[https:~~/~~/www.brainsimulation.org>>url:https://www.brainsimulation.org/]]
	87	\|=Documentation\|[[https:~~/~~/drive.google.com/file/d/1VcXf3GX3KoihF4UzJQXzuGL4XWoqj5Jr/view>>url:https://drive.google.com/file/d/1VcXf3GX3KoihF4UzJQXzuGL4XWoqj5Jr/view]]
	88	\|=Support\|[[petra.ritter@charite.de>>path:mailto:petra.ritter@charite.de]]
	89	\|=Source Code\|[[https:~~/~~/hub.docker.com/r/thevirtualbrain/tvb_converter>>url:https://hub.docker.com/r/thevirtualbrain/tvb_converter]]
	90	\|=Download Page\|[[https:~~/~~/hub.docker.com/r/thevirtualbrain/tvb_converter>>url:https://hub.docker.com/r/thevirtualbrain/tvb_converter]]
	91	\|=License\|GPLv3
	92	\|=Current Version\|1.0
	93	\|=All Versions\|(((
	94	* 1.0
	95	)))
20.1	96
24.1	97	=== ===
23.1	98
21.1	99	== Publications on TVB/brain model preprocessing ==
20.1	100
	101	* [[https:~~/~~/www.ncbi.nlm.nih.gov/pubmed/25837600>>url:https://www.ncbi.nlm.nih.gov/pubmed/25837600]]
	102	* [[https:~~/~~/www.ncbi.nlm.nih.gov/pubmed/27480624>>url:https://www.ncbi.nlm.nih.gov/pubmed/27480624]]
26.1	103
	104	== Citing this work ==
	105
	106
44.1	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).
26.1	108
	109
28.1	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]]
26.1	111
	112
29.1	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.
28.1	114
	115
44.1	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
26.1	119	Smith, R., & Connelly, A. (2019). MRtrix3_connectome: A BIDS Application for quantitative structural connectome construction. //OHBM//, W610.
	120
	121
	122	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
1.1	123	)))
	124
26.1	125	== ==
1.1	126
	127	(% class="col-xs-12 col-sm-4" %)
	128	(((
	129	{{box title="Contents"}}
	130	{{toc/}}
	131	{{/box}}
	132
	133
	134	)))
	135	)))