Wiki source code of TVB PIPELINE
Last modified by ldomide on 2024/05/20 08:56
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| 5 | == TVB Image Processing Pipeline == | ||
| 6 | |||
| 7 | ==== [[Pipeline Video Tutorial>>https://drive.google.com/file/d/1VcXf3GX3KoihF4UzJQXzuGL4XWoqj5Jr/view||rel="noopener noreferrer" target="_blank"]] ==== | ||
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| 9 | ==== [[Direct link to notebook>>https://drive.ebrains.eu/d/5e2fbc74575c47e88780/||rel="noopener noreferrer" target="_blank"]] ==== | ||
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| 11 | [[image:8677353.png||style="float:left"]] | ||
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| 21 | == Quick links == | ||
| 22 | |||
| 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"]] | ||
| 26 | * [[User Story>>url:https://wiki.ebrains.eu/bin/view/Collabs/user-story-tvb/]] | ||
| 27 | |||
| 28 | == What can I find here? == | ||
| 29 | |||
| 30 | * the code underlying the pipeline including the orchestrator that manages processing on the supercomputer | ||
| 31 | * an IPython notebook that describes how to | ||
| 32 | ** use the TVB processing pipeline on one of the associated supercomputers using PyUnicore | ||
| 33 | ** upload MRI data to the supercomputer | ||
| 34 | ** set up and run the pipeline | ||
| 35 | ** download processing results | ||
| 36 | |||
| 37 | == What does the TVB processing pipeline do? == | ||
| 38 | |||
| 39 | After uploading MRI data to the supercomputer, the pipeline runs the three containers | ||
| 40 | |||
| 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"]] | ||
| 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 | |||
| 47 | == How do I use it? == | ||
| 48 | |||
| 49 | * the pipeline is implemented by three Docker containers (mrtrix3_connectome, fmriprep and tvb_converter) | ||
| 50 | * the containers can be executed on supercomputers and operated via IPython notebooks | ||
| 51 | * Find the notebook by clicking on "Drive" in the left menu. The notebook is located in the folder "notebooks" | ||
| 52 | * Direct link to notebook: [[https:~~/~~/drive.ebrains.eu/d/5e2fbc74575c47e88780/>>https://drive.ebrains.eu/d/5e2fbc74575c47e88780/]] | ||
| 53 | * To use the notebook, download it onto your local filesystem, create a new Collab and upload it there. | ||
| 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. | ||
| 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'" | ||
| 56 | |||
| 57 | == Metadata == | ||
| 58 | |||
| 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 | ))) | ||
| 96 | |||
| 97 | === === | ||
| 98 | |||
| 99 | == Publications on TVB/brain model preprocessing == | ||
| 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]] | ||
| 103 | |||
| 104 | == Citing this work == | ||
| 105 | |||
| 106 | |||
| 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). | ||
| 108 | |||
| 109 | |||
| 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]] | ||
| 111 | |||
| 112 | |||
| 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. | ||
| 114 | |||
| 115 | |||
| 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 | |||
| 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 | ||
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| 124 | |||
| 125 | == == | ||
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| 129 | {{box title="**Contents**"}} | ||
| 130 | {{toc/}} | ||
| 131 | {{/box}} | ||
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