Changes for page TVB PIPELINE

Last modified by ldomide on 2024/05/20 08:56
From version 25.1
edited by michaels
on 2020/06/02 11:26
Change comment: There is no comment for this version
To version 17.1
edited by michaels
on 2020/05/06 13:44
Change comment: There is no comment for this version

Summary

Details

Page properties
Content
... ... @@ -6,13 +6,12 @@
6 6  
7 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 +[[image:8677353.png||style="float:left"]]
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 +== ==
12 12  
13 +== ==
13 13  
14 -[[image:8677353.png||style="float:left"]]
15 -
16 16  == ==
17 17  
18 18  == ==
... ... @@ -23,11 +23,16 @@
23 23  
24 24  == ==
25 25  
25 +(% class="wikigeneratedid" %)
26 26  == ==
27 27  
28 +(% class="wikigeneratedid" %)
28 28  == ==
29 29  
31 +(% class="wikigeneratedid" %)
30 30  == ==
33 +
34 +== [[Pipeline Video Tutorial>>https://drive.google.com/file/d/1VcXf3GX3KoihF4UzJQXzuGL4XWoqj5Jr/view||rel="noopener noreferrer" target="_blank"]] ==
31 31  )))
32 32  )))
33 33  
... ... @@ -38,21 +38,11 @@
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
45 +** use the TVB pipeline on one of the associated supercomputers using PyUnicore
46 +** 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)
... ... @@ -62,56 +62,9 @@
62 62  * To use the notebook, download it onto your local filesystem, create a new Collab and upload it there.
63 63  * Then, head over to [[https:~~/~~/lab.ebrains.eu/>>url:https://lab.ebrains.eu/||rel="noopener noreferrer" target="_blank"]] to edit and run your notebook.
64 64  * 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'"
65 -
66 -== Metadata ==
67 -
68 -|=Category|tool
69 -|=Tags|(((
70 -* [[Simulaton>>url:https://services.humanbrainproject.eu/software-catalog/catalog/?ctx=97d59245-adce-42c4-8b50-d22587071fcd&ctxstate=search%2Ctvb]]
71 -* [[TVB>>url:https://services.humanbrainproject.eu/software-catalog/catalog/?ctx=97d59245-adce-42c4-8b50-d22587071fcd&ctxstate=search%2Ctvb]]
72 -* [[visualization>>url:https://services.humanbrainproject.eu/software-catalog/catalog/?ctx=97d59245-adce-42c4-8b50-d22587071fcd&ctxstate=search%2Ctvb]]
73 -* [[open-source>>url:https://services.humanbrainproject.eu/software-catalog/catalog/?ctx=97d59245-adce-42c4-8b50-d22587071fcd&ctxstate=search%2Ctvb]]
74 -* [[analysis>>url:https://services.humanbrainproject.eu/software-catalog/catalog/?ctx=97d59245-adce-42c4-8b50-d22587071fcd&ctxstate=search%2Ctvb]]
75 -* [[supercomputers>>url:https://services.humanbrainproject.eu/software-catalog/catalog/?ctx=97d59245-adce-42c4-8b50-d22587071fcd&ctxstate=search%2Ctvb]]
76 -* [[brain-model>>url:https://services.humanbrainproject.eu/software-catalog/catalog/?ctx=97d59245-adce-42c4-8b50-d22587071fcd&ctxstate=search%2Ctvb]]
77 -* [[neuroinformatics>>url:https://services.humanbrainproject.eu/software-catalog/catalog/?ctx=97d59245-adce-42c4-8b50-d22587071fcd&ctxstate=search%2Ctvb]]
78 -* [[image-segmentation>>url:https://services.humanbrainproject.eu/software-catalog/catalog/?ctx=97d59245-adce-42c4-8b50-d22587071fcd&ctxstate=search%2Ctvb]]
79 -* [[simulation>>url:https://services.humanbrainproject.eu/software-catalog/catalog/?ctx=97d59245-adce-42c4-8b50-d22587071fcd&ctxstate=search%2Ctvb]]
80 -* [[The-Virtual-Brain>>url:https://services.humanbrainproject.eu/software-catalog/catalog/?ctx=97d59245-adce-42c4-8b50-d22587071fcd&ctxstate=search%2Ctvb]]
81 81  )))
82 -|=Partners|(((
83 -* Charité Universitätsmedizin Berlin [[CHARITE>>url:https://services.humanbrainproject.eu/software-catalog/catalog/?ctx=97d59245-adce-42c4-8b50-d22587071fcd&ctxstate=search%2Ctvb]]
84 -)))
85 -|=Maintainers|(((
86 -* [[Petra Ritter>>path:mailto:petra.ritter@charite.de]]
87 -* [[Michael Schirner>>path:mailto:michael.schirner@charite.de]]
88 -* [[Paul Triebkorn>>path:mailto:jan-paul.triebkorn@charite.de]]
89 -)))
90 -|=Contributors|(((
91 -* [[Petra Ritter>>path:mailto:petra.ritter@charite.de]]
92 -* [[Michael Schirner>>path:mailto:michael.schirner@charite.de]]
93 -* [[Paul Triebkorn>>path:mailto:jan-paul.triebkorn@charite.de]]
94 -)))
95 -|=Homepage|[[https:~~/~~/www.brainsimulation.org>>url:https://www.brainsimulation.org/]]
96 -|=Documentation|[[https:~~/~~/drive.google.com/file/d/1VcXf3GX3KoihF4UzJQXzuGL4XWoqj5Jr/view>>url:https://drive.google.com/file/d/1VcXf3GX3KoihF4UzJQXzuGL4XWoqj5Jr/view]]
97 -|=Support|[[petra.ritter@charite.de>>path:mailto:petra.ritter@charite.de]]
98 -|=Source Code|[[https:~~/~~/hub.docker.com/r/thevirtualbrain/tvb_converter>>url:https://hub.docker.com/r/thevirtualbrain/tvb_converter]]
99 -|=Download Page|[[https:~~/~~/hub.docker.com/r/thevirtualbrain/tvb_converter>>url:https://hub.docker.com/r/thevirtualbrain/tvb_converter]]
100 -|=License|GPLv3
101 -|=Current Version|1.0
102 -|=All Versions|(((
103 -* 1.0
104 -)))
105 105  
106 -=== ===
107 107  
108 -== Publications on TVB/brain model preprocessing ==
109 -
110 -* [[https:~~/~~/www.ncbi.nlm.nih.gov/pubmed/25837600>>url:https://www.ncbi.nlm.nih.gov/pubmed/25837600]]
111 -* [[https:~~/~~/www.ncbi.nlm.nih.gov/pubmed/27480624>>url:https://www.ncbi.nlm.nih.gov/pubmed/27480624]]
112 -)))
113 -
114 -
115 115  (% class="col-xs-12 col-sm-4" %)
116 116  (((
117 117  {{box title="**Contents**"}}
Public

TVB PIPELINE