Wiki source code of TVB PIPELINE

Version 32.1 by michaels on 2020/06/26 12:24

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30.1	5	= TVB Image Processing Pipeline With MINDS annotated Outputs =
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18.1	7	== [[Pipeline Video Tutorial>>https://drive.google.com/file/d/1VcXf3GX3KoihF4UzJQXzuGL4XWoqj5Jr/view\|\|rel="noopener noreferrer" target="_blank"]] ==
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23.1	9	== [[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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8.1	21	== What can I find here? ==
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7.1	23	* an IPython notebook that describes how to
25.1	24	** use the TVB processing pipeline on one of the associated supercomputers using PyUnicore
	25	** upload MRI data to the supercomputer
7.1	26	** set up and run the pipeline
	27	** download processing results
8.1	28
25.1	29	== What does the TVB processing pipeline do? ==
	30
	31	After uploading MRI data to the supercomputer, the pipeline runs the three containers
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26.1	33	* [[bids/mrtrix3_connectome>>https://hub.docker.com/r/bids/mrtrix3_connectome\|\|rel="noopener noreferrer" target="_blank"]]
	34	* [[poldracklab/fmriprep>>https://hub.docker.com/r/poldracklab/fmriprep\|\|rel="noopener noreferrer" target="_blank"]], and
	35	* [[thevirtualbrain/tvb_converter>>https://hub.docker.com/r/thevirtualbrain/tvb_converter\|\|rel="noopener noreferrer" target="_blank"]]
25.1	36
	37	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	39	== How do I use it? ==
	40
	41	* the pipeline is implemented by three Docker containers (mrtrix3_connectome, fmriprep and tvb_converter)
	42	* the containers are executed on supercomputers and operated via IPython notebooks
	43	* Find the notebook by clicking on "Drive" in the left menu. The notebook is located in the folder "notebooks"
10.1	44	* 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	45	* To use the notebook, download it onto your local filesystem, create a new Collab and upload it there.
10.1	46	* 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	47	* 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	48
	49	== Metadata ==
	50
23.1	51	\|=Category\|tool
	52	\|=Tags\|(((
	53	* [[Simulaton>>url:https://services.humanbrainproject.eu/software-catalog/catalog/?ctx=97d59245-adce-42c4-8b50-d22587071fcd&ctxstate=search%2Ctvb]]
	54	* [[TVB>>url:https://services.humanbrainproject.eu/software-catalog/catalog/?ctx=97d59245-adce-42c4-8b50-d22587071fcd&ctxstate=search%2Ctvb]]
	55	* [[visualization>>url:https://services.humanbrainproject.eu/software-catalog/catalog/?ctx=97d59245-adce-42c4-8b50-d22587071fcd&ctxstate=search%2Ctvb]]
	56	* [[open-source>>url:https://services.humanbrainproject.eu/software-catalog/catalog/?ctx=97d59245-adce-42c4-8b50-d22587071fcd&ctxstate=search%2Ctvb]]
	57	* [[analysis>>url:https://services.humanbrainproject.eu/software-catalog/catalog/?ctx=97d59245-adce-42c4-8b50-d22587071fcd&ctxstate=search%2Ctvb]]
	58	* [[supercomputers>>url:https://services.humanbrainproject.eu/software-catalog/catalog/?ctx=97d59245-adce-42c4-8b50-d22587071fcd&ctxstate=search%2Ctvb]]
	59	* [[brain-model>>url:https://services.humanbrainproject.eu/software-catalog/catalog/?ctx=97d59245-adce-42c4-8b50-d22587071fcd&ctxstate=search%2Ctvb]]
	60	* [[neuroinformatics>>url:https://services.humanbrainproject.eu/software-catalog/catalog/?ctx=97d59245-adce-42c4-8b50-d22587071fcd&ctxstate=search%2Ctvb]]
	61	* [[image-segmentation>>url:https://services.humanbrainproject.eu/software-catalog/catalog/?ctx=97d59245-adce-42c4-8b50-d22587071fcd&ctxstate=search%2Ctvb]]
	62	* [[simulation>>url:https://services.humanbrainproject.eu/software-catalog/catalog/?ctx=97d59245-adce-42c4-8b50-d22587071fcd&ctxstate=search%2Ctvb]]
	63	* [[The-Virtual-Brain>>url:https://services.humanbrainproject.eu/software-catalog/catalog/?ctx=97d59245-adce-42c4-8b50-d22587071fcd&ctxstate=search%2Ctvb]]
	64	)))
	65	\|=Partners\|(((
	66	* Charité Universitätsmedizin Berlin [[CHARITE>>url:https://services.humanbrainproject.eu/software-catalog/catalog/?ctx=97d59245-adce-42c4-8b50-d22587071fcd&ctxstate=search%2Ctvb]]
	67	)))
	68	\|=Maintainers\|(((
	69	* [[Petra Ritter>>path:mailto:petra.ritter@charite.de]]
	70	* [[Michael Schirner>>path:mailto:michael.schirner@charite.de]]
	71	* [[Paul Triebkorn>>path:mailto:jan-paul.triebkorn@charite.de]]
	72	)))
	73	\|=Contributors\|(((
	74	* [[Petra Ritter>>path:mailto:petra.ritter@charite.de]]
	75	* [[Michael Schirner>>path:mailto:michael.schirner@charite.de]]
	76	* [[Paul Triebkorn>>path:mailto:jan-paul.triebkorn@charite.de]]
	77	)))
	78	\|=Homepage\|[[https:~~/~~/www.brainsimulation.org>>url:https://www.brainsimulation.org/]]
	79	\|=Documentation\|[[https:~~/~~/drive.google.com/file/d/1VcXf3GX3KoihF4UzJQXzuGL4XWoqj5Jr/view>>url:https://drive.google.com/file/d/1VcXf3GX3KoihF4UzJQXzuGL4XWoqj5Jr/view]]
	80	\|=Support\|[[petra.ritter@charite.de>>path:mailto:petra.ritter@charite.de]]
	81	\|=Source Code\|[[https:~~/~~/hub.docker.com/r/thevirtualbrain/tvb_converter>>url:https://hub.docker.com/r/thevirtualbrain/tvb_converter]]
	82	\|=Download Page\|[[https:~~/~~/hub.docker.com/r/thevirtualbrain/tvb_converter>>url:https://hub.docker.com/r/thevirtualbrain/tvb_converter]]
	83	\|=License\|GPLv3
	84	\|=Current Version\|1.0
	85	\|=All Versions\|(((
	86	* 1.0
	87	)))
20.1	88
24.1	89	=== ===
23.1	90
21.1	91	== Publications on TVB/brain model preprocessing ==
20.1	92
	93	* [[https:~~/~~/www.ncbi.nlm.nih.gov/pubmed/25837600>>url:https://www.ncbi.nlm.nih.gov/pubmed/25837600]]
	94	* [[https:~~/~~/www.ncbi.nlm.nih.gov/pubmed/27480624>>url:https://www.ncbi.nlm.nih.gov/pubmed/27480624]]
26.1	95
	96	== Citing this work ==
	97
	98
	99	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).
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28.1	102	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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	104
29.1	105	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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26.1	108	Smith, R., & Connelly, A. (2019). MRtrix3_connectome: A BIDS Application for quantitative structural connectome construction. //OHBM//, W610.
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	111	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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