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6	6
7	7	Neuroimaging data preprocessing pipeline
8	8
9		-== [[Pipeline Video Tutorial>>https://drive.google.com/file/d/1VcXf3GX3KoihF4UzJQXzuGL4XWoqj5Jr/view||rel="noopener noreferrer" target="_blank"]] ==
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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	+== ==
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14		-[[image:8677353.png||style="float:left"]]
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24	24	== ==
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	25	+(% class="wikigeneratedid" %)
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	28	+(% class="wikigeneratedid" %)
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	33	+
	34	+== [[Pipeline Video Tutorial>>https://drive.google.com/file/d/1VcXf3GX3KoihF4UzJQXzuGL4XWoqj5Jr/view||rel="noopener noreferrer" target="_blank"]] ==
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38	38	== What can I find here? ==
39	39
40	40	* an IPython notebook that describes how to
41		-** use the TVB processing pipeline on one of the associated supercomputers using PyUnicore
42		-** upload MRI data to the supercomputer
	45	+** use the TVB pipeline on one of the associated supercomputers using PyUnicore
	46	+** upload model data to the supercomputer
43	43	** set up and run the pipeline
44	44	** download processing results
45	45
46		-== What does the TVB processing pipeline do? ==
47		-
48		-After uploading MRI data to the supercomputer, the pipeline runs the three containers
49		-
50		-* [[bids/mrtrix3_connectome>>https://hub.docker.com/r/bids/mrtrix3_connectome||rel="noopener noreferrer" target="_blank"]]
51		-* [[poldracklab/fmriprep>>https://hub.docker.com/r/poldracklab/fmriprep||rel="noopener noreferrer" target="_blank"]], and
52		-* [[thevirtualbrain/tvb_converter>>https://hub.docker.com/r/thevirtualbrain/tvb_converter||rel="noopener noreferrer" target="_blank"]]
53		-
54		-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.
55		-
56	56	== How do I use it? ==
57	57
58	58	* the pipeline is implemented by three Docker containers (mrtrix3_connectome, fmriprep and tvb_converter)
...	...	@@ -62,72 +62,9 @@
62	62	* To use the notebook, download it onto your local filesystem, create a new Collab and upload it there.
63	63	* Then, head over to [[https:~~/~~/lab.ebrains.eu/>>url:https://lab.ebrains.eu/||rel="noopener noreferrer" target="_blank"]] to edit and run your notebook.
64	64	* 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'"
65		-
66		-== Metadata ==
67		-
68		-|=Category|tool
69		-|=Tags|(((
70		-* [[Simulaton>>url:https://services.humanbrainproject.eu/software-catalog/catalog/?ctx=97d59245-adce-42c4-8b50-d22587071fcd&ctxstate=search%2Ctvb]]
71		-* [[TVB>>url:https://services.humanbrainproject.eu/software-catalog/catalog/?ctx=97d59245-adce-42c4-8b50-d22587071fcd&ctxstate=search%2Ctvb]]
72		-* [[visualization>>url:https://services.humanbrainproject.eu/software-catalog/catalog/?ctx=97d59245-adce-42c4-8b50-d22587071fcd&ctxstate=search%2Ctvb]]
73		-* [[open-source>>url:https://services.humanbrainproject.eu/software-catalog/catalog/?ctx=97d59245-adce-42c4-8b50-d22587071fcd&ctxstate=search%2Ctvb]]
74		-* [[analysis>>url:https://services.humanbrainproject.eu/software-catalog/catalog/?ctx=97d59245-adce-42c4-8b50-d22587071fcd&ctxstate=search%2Ctvb]]
75		-* [[supercomputers>>url:https://services.humanbrainproject.eu/software-catalog/catalog/?ctx=97d59245-adce-42c4-8b50-d22587071fcd&ctxstate=search%2Ctvb]]
76		-* [[brain-model>>url:https://services.humanbrainproject.eu/software-catalog/catalog/?ctx=97d59245-adce-42c4-8b50-d22587071fcd&ctxstate=search%2Ctvb]]
77		-* [[neuroinformatics>>url:https://services.humanbrainproject.eu/software-catalog/catalog/?ctx=97d59245-adce-42c4-8b50-d22587071fcd&ctxstate=search%2Ctvb]]
78		-* [[image-segmentation>>url:https://services.humanbrainproject.eu/software-catalog/catalog/?ctx=97d59245-adce-42c4-8b50-d22587071fcd&ctxstate=search%2Ctvb]]
79		-* [[simulation>>url:https://services.humanbrainproject.eu/software-catalog/catalog/?ctx=97d59245-adce-42c4-8b50-d22587071fcd&ctxstate=search%2Ctvb]]
80		-* [[The-Virtual-Brain>>url:https://services.humanbrainproject.eu/software-catalog/catalog/?ctx=97d59245-adce-42c4-8b50-d22587071fcd&ctxstate=search%2Ctvb]]
81	81	)))
82		-|=Partners|(((
83		-* Charité Universitätsmedizin Berlin [[CHARITE>>url:https://services.humanbrainproject.eu/software-catalog/catalog/?ctx=97d59245-adce-42c4-8b50-d22587071fcd&ctxstate=search%2Ctvb]]
84		-)))
85		-|=Maintainers|(((
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		-|=Contributors|(((
91		-* [[Petra Ritter>>path:mailto:petra.ritter@charite.de]]
92		-* [[Michael Schirner>>path:mailto:michael.schirner@charite.de]]
93		-* [[Paul Triebkorn>>path:mailto:jan-paul.triebkorn@charite.de]]
94		-)))
95		-|=Homepage|[[https:~~/~~/www.brainsimulation.org>>url:https://www.brainsimulation.org/]]
96		-|=Documentation|[[https:~~/~~/drive.google.com/file/d/1VcXf3GX3KoihF4UzJQXzuGL4XWoqj5Jr/view>>url:https://drive.google.com/file/d/1VcXf3GX3KoihF4UzJQXzuGL4XWoqj5Jr/view]]
97		-|=Support|[[petra.ritter@charite.de>>path:mailto:petra.ritter@charite.de]]
98		-|=Source Code|[[https:~~/~~/hub.docker.com/r/thevirtualbrain/tvb_converter>>url:https://hub.docker.com/r/thevirtualbrain/tvb_converter]]
99		-|=Download Page|[[https:~~/~~/hub.docker.com/r/thevirtualbrain/tvb_converter>>url:https://hub.docker.com/r/thevirtualbrain/tvb_converter]]
100		-|=License|GPLv3
101		-|=Current Version|1.0
102		-|=All Versions|(((
103		-* 1.0
104		-)))
105	105
106		-=== ===
107	107
108		-== Publications on TVB/brain model preprocessing ==
109		-
110		-* [[https:~~/~~/www.ncbi.nlm.nih.gov/pubmed/25837600>>url:https://www.ncbi.nlm.nih.gov/pubmed/25837600]]
111		-* [[https:~~/~~/www.ncbi.nlm.nih.gov/pubmed/27480624>>url:https://www.ncbi.nlm.nih.gov/pubmed/27480624]]
112		-
113		-
114		-== Citing this work ==
115		-
116		-
117		-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).
118		-
119		-
120		-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
121		-
122		-
123		-Smith, R., & Connelly, A. (2019). MRtrix3_connectome: A BIDS Application for quantitative structural connectome construction. //OHBM//, W610.
124		-
125		-
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
127		-)))
128		-
129		-== ==
130		-
131	131	(% class="col-xs-12 col-sm-4" %)
132	132	(((
133	133	{{box title="**Contents**"}}