graphvar: a user-friendly toolbox for comprehensive graph
TRANSCRIPT
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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
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The Analysis Setup GUI
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Setup panel
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Workflows
Statistical analyses (GLM) with clinical
data
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Workflows
Calculate and export graph metrics
Statistics on raw matrix
Statistics with
graph
metrics
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Setup panel (mouse over help)
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Parallel Computing (with toolbox)
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Setup panel
Underlying codes from the Brain Connectivity Toolbox (Rubinov and Sporns, 2010)
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General settings
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Load (existing) Connectivity Matrices
Subject´s Association Matrices
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Generate Connectivity Matrices
Individual nodal time courses
Node 1 Node 2 Node 3 Node n
Tim
e c
ou
rse…
Tim
e c
ou
rse…
Tim
e c
ou
rse…
Tim
e c
ou
rse…
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Label nodes
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Variable Selection
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Network construction
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Network nodes
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Redefine Network (Subnetwork analyses)
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Network thresholds
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Subject specific null model networks
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Network topological measures
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Export network topological measures
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Statistical analyses (GLM)
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Non-parametric testing
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Statistical analyses of graph measures
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Statistics on the raw conn matrices
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Network-Based-Statistics
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Create Connectivity matrix -> sliding windows
Generate the Sliding Window matrices with the „connectivity“
measure you desire:
- Pearson corr - Partial corr - Covariance - Mutual inf
- etc…..
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Select dynamic summary measure (graph metrics/raw matrix)
If SW-matrices are loaded (also manually via „Select Subjects Corr Matrix“) the
dynamic selection windows will appear in the GUI
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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
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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
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Ready to go!
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Status bar
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The Results Viewer GUI
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Results selection box
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General functions panel
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Correction for multiple comparisons
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Interpreting GraphVar output
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
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One dimensional graph metrics
Thresholds
Asso
ciation
to d
ep
en
de
nt variab
le
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One dimensional graph metrics
Non paramteric testing with random networks
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Two dimensional graph metrics
Thre
sho
lds
Network nodes
Ass
oci
atio
n t
o d
ep
en
de
nt
vari
able
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Three dimensional graph metrics
Network nodes
Netw
ork n
od
es
Ass
oci
atio
n t
o d
ep
en
de
nt
vari
able
Thresholds
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Associations to Rich club coefficients
level k
Netw
ork Th
resh
old
s A
sso
ciat
ion
to
de
pe
nd
en
t va
riab
le
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Export Results
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Plot single subject association matrices
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Plot mean connectivity matrix across subjects
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Identify Graph Components
Show graph component with Network Inspector
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Network Inspector GUI
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Identify Graph Components
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Mouse over
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Show association strenght
Show association to dependent variable
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Open directly in BrainNetViewer (Xia et al., 2013; PlosONE)
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GraphVar -Team