Wiki source code of TVB PIPELINE
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| 5 | = TVB Image Processing Pipeline With MINDS annotated Outputs = | ||
| 6 | |||
| 7 | == [[Pipeline Video Tutorial>>https://drive.google.com/file/d/1VcXf3GX3KoihF4UzJQXzuGL4XWoqj5Jr/view||rel="noopener noreferrer" target="_blank"]] == | ||
| 8 | |||
| 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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| 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 | * an IPython notebook that describes how to | ||
| 31 | ** use the TVB processing pipeline on one of the associated supercomputers using PyUnicore | ||
| 32 | ** upload MRI data to the supercomputer | ||
| 33 | ** set up and run the pipeline | ||
| 34 | ** download processing results | ||
| 35 | |||
| 36 | == What does the TVB processing pipeline do? == | ||
| 37 | |||
| 38 | After uploading MRI data to the supercomputer, the pipeline runs the three containers | ||
| 39 | |||
| 40 | * [[bids/mrtrix3_connectome>>https://hub.docker.com/r/bids/mrtrix3_connectome||rel="noopener noreferrer" target="_blank"]] | ||
| 41 | * [[poldracklab/fmriprep>>https://hub.docker.com/r/poldracklab/fmriprep||rel="noopener noreferrer" target="_blank"]], and | ||
| 42 | * [[thevirtualbrain/tvb_converter>>https://hub.docker.com/r/thevirtualbrain/tvb_converter||rel="noopener noreferrer" target="_blank"]] | ||
| 43 | |||
| 44 | 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. | ||
| 45 | |||
| 46 | == How do I use it? == | ||
| 47 | |||
| 48 | * the pipeline is implemented by three Docker containers (mrtrix3_connectome, fmriprep and tvb_converter) | ||
| 49 | * the containers are executed on supercomputers and operated via IPython notebooks | ||
| 50 | * Find the notebook by clicking on "Drive" in the left menu. The notebook is located in the folder "notebooks" | ||
| 51 | * 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]] | ||
| 52 | * To use the notebook, download it onto your local filesystem, create a new Collab and upload it there. | ||
| 53 | * Then, head over to [[https:~~/~~/lab.ebrains.eu/>>url:https://lab.ebrains.eu/||rel="noopener noreferrer" target="_blank"]] to edit and run your notebook. | ||
| 54 | * 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'" | ||
| 55 | |||
| 56 | == Metadata == | ||
| 57 | |||
| 58 | |=Category|tool | ||
| 59 | |=Tags|((( | ||
| 60 | * [[Simulaton>>url:https://services.humanbrainproject.eu/software-catalog/catalog/?ctx=97d59245-adce-42c4-8b50-d22587071fcd&ctxstate=search%2Ctvb]] | ||
| 61 | * [[TVB>>url:https://services.humanbrainproject.eu/software-catalog/catalog/?ctx=97d59245-adce-42c4-8b50-d22587071fcd&ctxstate=search%2Ctvb]] | ||
| 62 | * [[visualization>>url:https://services.humanbrainproject.eu/software-catalog/catalog/?ctx=97d59245-adce-42c4-8b50-d22587071fcd&ctxstate=search%2Ctvb]] | ||
| 63 | * [[open-source>>url:https://services.humanbrainproject.eu/software-catalog/catalog/?ctx=97d59245-adce-42c4-8b50-d22587071fcd&ctxstate=search%2Ctvb]] | ||
| 64 | * [[analysis>>url:https://services.humanbrainproject.eu/software-catalog/catalog/?ctx=97d59245-adce-42c4-8b50-d22587071fcd&ctxstate=search%2Ctvb]] | ||
| 65 | * [[supercomputers>>url:https://services.humanbrainproject.eu/software-catalog/catalog/?ctx=97d59245-adce-42c4-8b50-d22587071fcd&ctxstate=search%2Ctvb]] | ||
| 66 | * [[brain-model>>url:https://services.humanbrainproject.eu/software-catalog/catalog/?ctx=97d59245-adce-42c4-8b50-d22587071fcd&ctxstate=search%2Ctvb]] | ||
| 67 | * [[neuroinformatics>>url:https://services.humanbrainproject.eu/software-catalog/catalog/?ctx=97d59245-adce-42c4-8b50-d22587071fcd&ctxstate=search%2Ctvb]] | ||
| 68 | * [[image-segmentation>>url:https://services.humanbrainproject.eu/software-catalog/catalog/?ctx=97d59245-adce-42c4-8b50-d22587071fcd&ctxstate=search%2Ctvb]] | ||
| 69 | * [[simulation>>url:https://services.humanbrainproject.eu/software-catalog/catalog/?ctx=97d59245-adce-42c4-8b50-d22587071fcd&ctxstate=search%2Ctvb]] | ||
| 70 | * [[The-Virtual-Brain>>url:https://services.humanbrainproject.eu/software-catalog/catalog/?ctx=97d59245-adce-42c4-8b50-d22587071fcd&ctxstate=search%2Ctvb]] | ||
| 71 | ))) | ||
| 72 | |=Partners|((( | ||
| 73 | * Charité Universitätsmedizin Berlin [[CHARITE>>url:https://services.humanbrainproject.eu/software-catalog/catalog/?ctx=97d59245-adce-42c4-8b50-d22587071fcd&ctxstate=search%2Ctvb]] | ||
| 74 | ))) | ||
| 75 | |=Maintainers|((( | ||
| 76 | * [[Petra Ritter>>path:mailto:petra.ritter@charite.de]] | ||
| 77 | * [[Michael Schirner>>path:mailto:michael.schirner@charite.de]] | ||
| 78 | * [[Paul Triebkorn>>path:mailto:jan-paul.triebkorn@charite.de]] | ||
| 79 | ))) | ||
| 80 | |=Contributors|((( | ||
| 81 | * [[Petra Ritter>>path:mailto:petra.ritter@charite.de]] | ||
| 82 | * [[Michael Schirner>>path:mailto:michael.schirner@charite.de]] | ||
| 83 | * [[Paul Triebkorn>>path:mailto:jan-paul.triebkorn@charite.de]] | ||
| 84 | ))) | ||
| 85 | |=Homepage|[[https:~~/~~/www.brainsimulation.org>>url:https://www.brainsimulation.org/]] | ||
| 86 | |=Documentation|[[https:~~/~~/drive.google.com/file/d/1VcXf3GX3KoihF4UzJQXzuGL4XWoqj5Jr/view>>url:https://drive.google.com/file/d/1VcXf3GX3KoihF4UzJQXzuGL4XWoqj5Jr/view]] | ||
| 87 | |=Support|[[petra.ritter@charite.de>>path:mailto:petra.ritter@charite.de]] | ||
| 88 | |=Source Code|[[https:~~/~~/hub.docker.com/r/thevirtualbrain/tvb_converter>>url:https://hub.docker.com/r/thevirtualbrain/tvb_converter]] | ||
| 89 | |=Download Page|[[https:~~/~~/hub.docker.com/r/thevirtualbrain/tvb_converter>>url:https://hub.docker.com/r/thevirtualbrain/tvb_converter]] | ||
| 90 | |=License|GPLv3 | ||
| 91 | |=Current Version|1.0 | ||
| 92 | |=All Versions|((( | ||
| 93 | * 1.0 | ||
| 94 | ))) | ||
| 95 | |||
| 96 | === === | ||
| 97 | |||
| 98 | == Publications on TVB/brain model preprocessing == | ||
| 99 | |||
| 100 | * [[https:~~/~~/www.ncbi.nlm.nih.gov/pubmed/25837600>>url:https://www.ncbi.nlm.nih.gov/pubmed/25837600]] | ||
| 101 | * [[https:~~/~~/www.ncbi.nlm.nih.gov/pubmed/27480624>>url:https://www.ncbi.nlm.nih.gov/pubmed/27480624]] | ||
| 102 | |||
| 103 | == Citing this work == | ||
| 104 | |||
| 105 | |||
| 106 | 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). | ||
| 107 | |||
| 108 | |||
| 109 | 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]] | ||
| 110 | |||
| 111 | |||
| 112 | 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. | ||
| 113 | |||
| 114 | |||
| 115 | Smith, R., & Connelly, A. (2019). MRtrix3_connectome: A BIDS Application for quantitative structural connectome construction. //OHBM//, W610. | ||
| 116 | |||
| 117 | |||
| 118 | 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 | ||
| 119 | ))) | ||
| 120 | |||
| 121 | == == | ||
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| 125 | {{box title="**Contents**"}} | ||
| 126 | {{toc/}} | ||
| 127 | {{/box}} | ||
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