Changes for page TVB PIPELINE

Last modified by ldomide on 2024/05/20 08:56
From version 33.1
edited by michaels
on 2020/07/06 09:37
Change comment: There is no comment for this version
To version 24.1
edited by michaels
on 2020/05/07 14:05
Change comment: There is no comment for this version

Summary

Details

Page properties
Content
... ... @@ -2,15 +2,32 @@
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 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  
13 +
11 11  [[image:8677353.png||style="float:left"]]
12 12  
13 -
16 +== ==
17 +
18 +== ==
19 +
20 +== ==
21 +
22 +== ==
23 +
24 +== ==
25 +
26 +== ==
27 +
28 +== ==
29 +
30 +== ==
14 14  )))
15 15  )))
16 16  
... ... @@ -18,31 +18,14 @@
18 18  (((
19 19  (% class="col-xs-12 col-sm-8" %)
20 20  (((
21 -== Quick links ==
22 -
23 -* [[TVB on EBRAINS (Short Version)>>url:https://www.youtube.com/watch?v=_G_DjRb1ams&feature=youtu.be]]
24 -* [[TVB on EBRAINS (Long Version)>>url:https://www.youtube.com/watch?v=eZrh6ztGFAY&feature=youtu.be]]
25 -* [[TVB on EBRAINS (Mini Videos)>>url:https://www.youtube.com/playlist?list=PLVtblERyzDeLcVv4BbW3BvmO8D-qVZxKf]]
26 -* [[User Story>>url:https://wiki.ebrains.eu/bin/view/Collabs/user-story-tvb/]]
27 -
28 28  == What can I find here? ==
29 29  
30 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
41 +** use the TVB pipeline on one of the associated supercomputers using PyUnicore
42 +** upload model data to the supercomputer
33 33  ** set up and run the pipeline
34 34  ** download processing results
35 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 46  == How do I use it? ==
47 47  
48 48  * the pipeline is implemented by three Docker containers (mrtrix3_connectome, fmriprep and tvb_converter)
... ... @@ -99,26 +99,8 @@
99 99  
100 100  * [[https:~~/~~/www.ncbi.nlm.nih.gov/pubmed/25837600>>url:https://www.ncbi.nlm.nih.gov/pubmed/25837600]]
101 101  * [[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
119 119  )))
120 120  
121 -== ==
122 122  
123 123  (% class="col-xs-12 col-sm-4" %)
124 124  (((
Collaboratory.Apps.Collab.Code.CollabClass[0]
Description
... ... @@ -1,1 +1,1 @@
1 -TVB Image Processing Pipeline With MINDS annotated Outputs
1 +Construct brain network models from empirical MRI data.
Public

TVB PIPELINE