Changes for page TVB PIPELINE

Last modified by ldomide on 2024/05/20 08:56
From version 26.1
edited by michaels
on 2020/06/12 10:43
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To version 24.1
edited by michaels
on 2020/05/07 14:05
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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
41 +** use the TVB pipeline on one of the associated supercomputers using PyUnicore
42 +** 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)
... ... @@ -109,24 +109,8 @@
109 109  
110 110  * [[https:~~/~~/www.ncbi.nlm.nih.gov/pubmed/25837600>>url:https://www.ncbi.nlm.nih.gov/pubmed/25837600]]
111 111  * [[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
127 127  )))
128 128  
129 -== ==
130 130  
131 131  (% class="col-xs-12 col-sm-4" %)
132 132  (((
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TVB PIPELINE