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GraphVar Turbo GLM QuickGuide

GraphVar is a user-friendly toolbox for analyzing functional brain connectivity graphs. It features pipelines for: (1) constructing graph networks from connectivity matrices; (2) calculating topological measures of networks; (3) generating subject-specific random networks; (4) performing statistical tests using a GLM framework. It allows calculations on raw connectivity matrices and dynamic graph analyses using sliding windows. Results can be explored interactively and visually. The toolbox draws on codes from the Brain Connectivity Toolbox and enables comprehensive graph analyses of functional brain connectivity data.

Uploaded by

Rogerio Urbano
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© © All Rights Reserved
Available Formats
Download as PDF, TXT or read online on Scribd
6 views

GraphVar Turbo GLM QuickGuide

GraphVar is a user-friendly toolbox for analyzing functional brain connectivity graphs. It features pipelines for: (1) constructing graph networks from connectivity matrices; (2) calculating topological measures of networks; (3) generating subject-specific random networks; (4) performing statistical tests using a GLM framework. It allows calculations on raw connectivity matrices and dynamic graph analyses using sliding windows. Results can be explored interactively and visually. The toolbox draws on codes from the Brain Connectivity Toolbox and enables comprehensive graph analyses of functional brain connectivity data.

Uploaded by

Rogerio Urbano
Copyright
© © All Rights Reserved
Available Formats
Download as PDF, TXT or read online on Scribd
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GraphVar: A user-friendly toolbox for comprehensive graph analyses of

functional brain connectivity.


• features:

I. Pipeline construction of graph networks


II. Calculation of network topological measures
III. Generation of subject specific random networks
IV. Perform statistical tests with a GLM framework
V. Calculations on raw connectivity matrices (Network based statistics)
VI. Parametric and non-parametric testing
VII. Dynamic graph analyses (sliding windows)
VIII. Interactive and visual results exploration

• Kruschwitz, J.D 1,2*, List, D. 1,2*, Waller, L. 2, Rubinov, M. 3, Walter, H 1.


*equal contribution
1 Charité Universitätsmedizin, Berlin, Germany
2 Technische Universität Dresden, Dresden, Germany
3 University of Cambridge, Cambridge, United Kingdom
The Analysis Setup GUI
Setup panel
Statistical analyses
(GLM) with clinical
data

Workflows
Calculate and export graph metrics

Statistics with graph metrics


Statistics on raw matrix

Workflows
Setup panel (mouse over help)
Parallel Computing (with toolbox)
Underlying codes from the Brain Connectivity Toolbox (Rubinov and Sporns, 2010)

Setup panel
General settings
Subject´s Association Matrices

Load (existing) Connectivity Matrices


Individual nodal time courses

Node 1 Node 2 Node 3 Node n

Time course…
Time course…

Time course…
Time course…

Generate Connectivity Matrices


Label nodes
Variable Selection
Network construction
Network nodes
Redefine Network (Subnetwork analyses)
Network thresholds
Subject specific null model networks
Network topological measures
Export network topological measures
Statistical analyses (GLM)
Non-parametric testing
Statistical analyses of graph measures
Statistics on the raw conn matrices
Network-Based-Statistics
Generate the Sliding Window
matrices with the „connectivity“
measure you desire:

- Pearson corr
- Partial corr
- Covariance
- Mutual inf
- etc…..

Create Connectivity matrix -> sliding windows


If SW-matrices are loaded
(also manually via „Select
Subjects Corr Matrix“) the
dynamic selection windows
will appear in the GUI

Select dynamic summary measure (graph metrics/raw matrix)


Dynamic summary
measures*:

- Variance
- Standard deviation
- Periodicity
- PointProcess: rate
- PointProcess: intervall
- Brain-Network Variability

* definition in Dynamic GraphVar Tutorial

Select dynamic summary measure (graph metrics/raw matrix)


GraphVar will perform all the
operations with respect to the
dynamic summary measure:

e.g. compute the variance of the


clustering coefficient across the
sliding windows and export or do
group statistics on this measure

Select dynamic summary measure (graph metrics/raw matrix)


Ready to go!
Status bar
The Results Viewer GUI
Results selection box
General functions panel
Correction for multiple comparisons
d: Difference between Group Means
F(df1,df2): F-value

d(b): Difference between Standardized


Regression Weights

b: Standardized Regression Weight


t(df): t-Value
p: p-Value

m: Mean
significant
not-significant

Interpreting GraphVar output


Association to dependent variable

Thresholds

One dimensional graph metrics


Non paramteric testing with
random networks

One dimensional graph metrics


Association to dependent variable
Thresholds

Network nodes

Two dimensional graph metrics


Thresholds

Association to dependent variable


Network nodes

Network nodes

Three dimensional graph metrics


Association to dependent variable
Network Thresholds

level k

Associations to Rich club coefficients


Export Results
Plot single subject association matrices
Plot mean connectivity matrix across subjects
Show graph component with
Network Inspector

Identify Graph Components


Network Inspector GUI
Identify Graph Components
Mouse over
Show association to
dependent variable

Show association strenght


Open directly in BrainNetViewer
(Xia et al., 2013; PlosONE)
GraphVar -Team

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