Changes for page User Story: TVB

Last modified by ldomide on 2024/05/20 08:51
From version 36.1
edited by evanhancock
on 2020/12/10 10:16
Change comment: There is no comment for this version
To version 42.1
edited by evanhancock
on 2021/04/16 21:40
Change comment: There is no comment for this version

Summary

Details

Page properties
Content
... ... @@ -13,9 +13,10 @@
13 13  * [[Series of mini videos>>https://www.youtube.com/playlist?list=PLVtblERyzDeLcVv4BbW3BvmO8D-qVZxKf]]
14 14  
15 15  [[image:export_overview_new2.png]]
16 +TVB on EBRAINS services.
16 16  )))
17 17  )))
18 -TVB on EBRAINS services.
19 +
19 19  (% class="row" %)
20 20  (((
21 21  (% class="col-xs-12 col-sm-8" %)
... ... @@ -25,11 +25,11 @@
25 25  [[image:Screenshot 2020-10-19 at 09.14.45.png]]
26 26  
27 27  (% class="wikigeneratedid" %)
28 -TVB on EBRAINS cloud infrastructure. Brain simulation and neuroimaging workflows require personal medical data that is applicable to data protection regulation. To protect personal data the services rely on
29 -end-to-end encryption and access control. EBRAINS provides several core services: 'Drive' is a service for hosting and sharing files; 'Wiki' and 'Office' allow users to create workspaces and documents for collaborative research; 'Lab' hosts sandboxed JupyterLab instances for running live code; 'OpenShift' orchestrates different services and provides resources for interactive computing; 'HPC' are supercomputing backends for resource-intensive computations. Core services interact with the different
30 -deployments of TVB services via a RESTful API and Unicore for communication with supercomputers. TVB services are deployed in the form of a Web GUI, container images, Python notebooks, Python libraries and high-performance backend codes. The TVB Image Processing Pipeline produces structural and functional connectomes from MRI data and its outputs can be ingested by KnowledgeGraph and annotated with openMINDS metadata, which allows re-using the connectomes in other services. The connectors show
31 -interactions between different components (colours group connectors for different deployments). The six TVB services are independent modules that can be combined according to the requirements of the research question.
29 +TVB on EBRAINS cloud infrastructure.
32 32  
31 +(% class="wikigeneratedid" %)
32 +Brain simulation and neuroimaging workflows require personal medical data that is applicable to data protection regulation. To protect personal data the services rely on end-to-end encryption and access control. EBRAINS provides several core services: 'Drive' is a service for hosting and sharing files; 'Wiki' and 'Office' allow users to create workspaces and documents for collaborative research; 'Lab' hosts sandboxed JupyterLab instances for running live code; 'OpenShift' orchestrates different services and provides resources for interactive computing; 'HPC' are supercomputing backends for resource-intensive computations. Core services interact with the different deployments of TVB services via a RESTful API and Unicore for communication with supercomputers. TVB services are deployed in the form of a Web GUI, container images, Python notebooks, Python libraries and high-performance backend codes. The TVB Image Processing Pipeline produces structural and functional connectomes from MRI data and its outputs can be ingested by KnowledgeGraph and annotated with openMINDS metadata, which allows re-using the connectomes in other services. The connectors show interactions between different components (colours group connectors for different deployments). The six TVB services are independent modules that can be combined according to the requirements of the research question.
33 +
33 33  == TVB pipeline: Extract connectomes ==
34 34  
35 35  As a first step we browse through The Knowledge Graph (KG) in order to find a suitable dataset to construct a brain model. The dataset must contain diffusion-weighted MRI data, in order to extract a structural connectome, which will form the basis of a brain network model. Structural connectivity extracted from diffusion MRI is used to quantify how strongly brain regions interact in the brain model. Next, the data set must contain functional MRI (fMRI) data, because a common approach is to tune the parameters of the brain model such that the simulated fMRI functional connectivity fits with the empirical fMRI data. For fitting, we usually compute functional connectivity matrices from simulated and empirical data. Finally, we need anatomical T1-weighted MRI to extract cortical surfaces and to perform a parcellation of the brain into different regions.
... ... @@ -45,7 +45,6 @@
45 45  
46 46  * Download the imaging data. The full dataset would be quite large: 54.06 GB. It contains several subjects, modalities, tasks and runs, most of which we don’t need to demo the workflow. We will therefore only download the minimal set of files that we need to form a valid BIDS data set and to perform the following steps. Using the Dataset File Tree on the right, download the files indicated in the following folder tree. The interface unfortunately only allows to download individual files, so you have to click each one of them and also you have to create the necessary folder structure (incl. the folders sub-01, anat, dwi, func) yourself. Note that the full data set contains multiple sessions identified by the keyword “ses-XX”, where “XX” indicates the session number. Here we use only data from ses-00 and therefore omit the folder and instead directly copy the folders “dwi”, “func”, and “anat” one level beneath “sub-01”. When you are done, your folder tree should look like this:
47 47  
48 -
49 49  [[image:tree.png]]
50 50  
51 51  Folder tree of the example data set.
XWiki.XWikiRights[5]
Allow/Deny
... ... @@ -1,1 +1,0 @@
1 -Allow
Levels
... ... @@ -1,1 +1,0 @@
1 -view
Users
... ... @@ -1,1 +1,0 @@
1 -XWiki.XWikiGuest
XWiki.XWikiRights[6]
Allow/Deny
... ... @@ -1,1 +1,0 @@
1 -Allow
Groups
... ... @@ -1,1 +1,0 @@
1 -XWiki.XWikiAllGroup
Levels
... ... @@ -1,1 +1,0 @@
1 -view
XWiki.XWikiRights[7]
Allow/Deny
... ... @@ -1,0 +1,1 @@
1 +Allow
Levels
... ... @@ -1,0 +1,1 @@
1 +view
Users
... ... @@ -1,0 +1,1 @@
1 +XWiki.XWikiGuest
XWiki.XWikiRights[8]
Allow/Deny
... ... @@ -1,0 +1,1 @@
1 +Allow
Groups
... ... @@ -1,0 +1,1 @@
1 +XWiki.XWikiAllGroup
Levels
... ... @@ -1,0 +1,1 @@
1 +view