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2	2	(((
3	3	(% class="container" %)
4	4	(((
5		-= TVB Image Processing Pipeline With MINDS annotated Outputs =
	5	+= From MRI to Functional and Structural Connectivity =
6	6
	7	+Neuroimaging data preprocessing pipeline
	8	+
7	7	== [[Pipeline Video Tutorial>>https://drive.google.com/file/d/1VcXf3GX3KoihF4UzJQXzuGL4XWoqj5Jr/view||rel="noopener noreferrer" target="_blank"]] ==
8	8
9		-== [[Direct link to notebook>>https://drive.ebrains.eu/#my-libs/lib/42ac27a5-981e-4cf6-8ec5-d67b0c24bf09/notebooks||rel="noopener noreferrer" target="_blank"]] ==
10	10
11	11	[[image:8677353.png||style="float:left"]]
12	12
13		-
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15	15	)))
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21	21	== What can I find here? ==
22	22
23	23	* an IPython notebook that describes how to
24		-** use the TVB processing pipeline on one of the associated supercomputers using PyUnicore
25		-** upload MRI data to the supercomputer
	39	+** use the TVB pipeline on one of the associated supercomputers using PyUnicore
	40	+** upload model data to the supercomputer
26	26	** set up and run the pipeline
27	27	** download processing results
28	28
29		-== What does the TVB processing pipeline do? ==
30		-
31		-After uploading MRI data to the supercomputer, the pipeline runs the three containers
32		-
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"]]
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.
38		-
39	39	== How do I use it? ==
40	40
41	41	* the pipeline is implemented by three Docker containers (mrtrix3_connectome, fmriprep and tvb_converter)
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48	48
49	49	== Metadata ==
50	50
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		-)))
	56	+* Partners: Charité Universitätsmedizin Berlin
	57	+* Developers: Michael Schirner (michael.schirner@charite.de), Paul Triebkorn
	58	+* Support: Petra Ritter (petra.ritter@charite.de)
	59	+* Homepage: [[https:~~/~~/www.brainsimulation.org>>url:https://www.brainsimulation.org/]]
	60	+* Documentation: [[https:~~/~~/drive.google.com/file/d/1VcXf3GX3KoihF4UzJQXzuGL4XWoqj5Jr/view>>https://drive.google.com/file/d/1VcXf3GX3KoihF4UzJQXzuGL4XWoqj5Jr/view]]
	61	+* Download as Docker image~: [[https:~~/~~/hub.docker.com/r/thevirtualbrain/tvb_converter>>url:https://hub.docker.com/r/thevirtualbrain/tvb_converter]]
	62	+* License: GPL3
	63	+* Version: 1.0
88	88
89		-=== ===
90		-
91	91	== Publications on TVB/brain model preprocessing ==
92	92
93	93	* [[https:~~/~~/www.ncbi.nlm.nih.gov/pubmed/25837600>>url:https://www.ncbi.nlm.nih.gov/pubmed/25837600]]
94	94	* [[https:~~/~~/www.ncbi.nlm.nih.gov/pubmed/27480624>>url:https://www.ncbi.nlm.nih.gov/pubmed/27480624]]
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).
100		-
101		-
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]]
103		-
104		-
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.
106		-
107		-
108		-Smith, R., & Connelly, A. (2019). MRtrix3_connectome: A BIDS Application for quantitative structural connectome construction. //OHBM//, W610.
109		-
110		-
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
112	112	)))
113	113
114		-== ==
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117	117	(((

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.