Changes for page TVB PIPELINE

Last modified by ldomide on 2024/05/20 08:56
From version 40.1
edited by michaels
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To version 24.1
edited by michaels
on 2020/05/07 14:05
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2 2  (((
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5 -== TVB Image Processing Pipeline ==
5 += From MRI to Functional and Structural Connectivity =
6 6  
7 -=== [[Web-GUI to configure and start processing on HPC>>https://thevirtualbrain.apps.hbp.eu/||target="_blank"]] ===
7 +Neuroimaging data preprocessing pipeline
8 8  
9 -==== [[Pipeline Video Tutorial>>https://drive.google.com/file/d/1VcXf3GX3KoihF4UzJQXzuGL4XWoqj5Jr/view||rel="noopener noreferrer" target="_blank"]] ====
9 +== [[Pipeline Video Tutorial>>https://drive.google.com/file/d/1VcXf3GX3KoihF4UzJQXzuGL4XWoqj5Jr/view||rel="noopener noreferrer" target="_blank"]] ==
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 +== [[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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23 -== Quick links ==
24 -
25 -* [[TVB on EBRAINS (Short Version)>>https://www.youtube.com/watch?v=EETRdGskiWQ&t=2s||rel="noopener noreferrer" target="_blank"]]
26 -* [[TVB on EBRAINS (Long Version)>>https://www.youtube.com/watch?v=VYhR9RNRIpA&t=2s||rel="noopener noreferrer" target="_blank"]]
27 -* [[TVB on EBRAINS (Mini Videos)>>url:https://www.youtube.com/playlist?list=PLVtblERyzDeLcVv4BbW3BvmO8D-qVZxKf||rel="noopener noreferrer" target="_blank"]]
28 -* [[User Story>>url:https://wiki.ebrains.eu/bin/view/Collabs/user-story-tvb/]]
29 -
30 30  == What can I find here? ==
31 31  
32 32  * an IPython notebook that describes how to
33 -** use the TVB processing pipeline on one of the associated supercomputers using PyUnicore
34 -** upload MRI data to the supercomputer
41 +** use the TVB pipeline on one of the associated supercomputers using PyUnicore
42 +** upload model data to the supercomputer
35 35  ** set up and run the pipeline
36 36  ** download processing results
37 37  
38 -== What does the TVB processing pipeline do? ==
39 -
40 -After uploading MRI data to the supercomputer, the pipeline runs the three containers
41 -
42 -* [[bids/mrtrix3_connectome>>https://hub.docker.com/r/bids/mrtrix3_connectome||rel="noopener noreferrer" target="_blank"]]
43 -* [[poldracklab/fmriprep>>https://hub.docker.com/r/poldracklab/fmriprep||rel="noopener noreferrer" target="_blank"]], and
44 -* [[thevirtualbrain/tvb_converter>>https://hub.docker.com/r/thevirtualbrain/tvb_converter||rel="noopener noreferrer" target="_blank"]]
45 -
46 -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.
47 -
48 48  == How do I use it? ==
49 49  
50 50  * the pipeline is implemented by three Docker containers (mrtrix3_connectome, fmriprep and tvb_converter)
51 -* the containers are executed on supercomputers and operated via the [[web GUI>>https://thevirtualbrain.apps.hbp.eu/]] or via IPython notebooks
49 +* the containers are executed on supercomputers and operated via IPython notebooks
52 52  * Find the notebook by clicking on "Drive" in the left menu. The notebook is located in the folder "notebooks"
53 53  * 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]]
54 54  * To use the notebook, download it onto your local filesystem, create a new Collab and upload it there.
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101 101  
102 102  * [[https:~~/~~/www.ncbi.nlm.nih.gov/pubmed/25837600>>url:https://www.ncbi.nlm.nih.gov/pubmed/25837600]]
103 103  * [[https:~~/~~/www.ncbi.nlm.nih.gov/pubmed/27480624>>url:https://www.ncbi.nlm.nih.gov/pubmed/27480624]]
104 -
105 -== Citing this work ==
106 -
107 -
108 -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).
109 -
110 -
111 -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]]
112 -
113 -
114 -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.  
115 -
116 -
117 -Smith, R., & Connelly, A. (2019). MRtrix3_connectome: A BIDS Application for quantitative structural connectome construction. //OHBM//, W610.
118 -
119 -
120 -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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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.
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TVB PIPELINE