Workflow

Graph analysis using BRAPH, can be accomplish with the following steps:

Figure 2: General workflow of BRAPH for MRI, fMRI, EEG, and PET data analysis. Each box represents a GUI available in BRAPH, while the arrows indicate the typical workflow. The formats of the BRAPH files are indicated within each box. The abbreviation WU refers to weighted udirected graphs, BUD to binary undirected graphs at a fixed density of connections, and BUT to binary undirected graphs at a fixed threshold.

General workflow of BRAPH for MRI, fMRI, EEG, and PET data analysis. Each box represents a GUI available in BRAPH, while the arrows indicate the typical workflow. The formats of the BRAPH files are indicated within each box. The abbreviation WU refers to weighted udirected graphs, BUD to binary undirected graphs at a fixed density of connections, and BUT to binary undirected graphs at a fixed threshold.

Brain Atlas

  • Defines the brain regions used for data analysis.
  • Input format: *.xlsx, *.txt ,*.xml, *.atlas
  • Output format: *.txt, *.xml, *.atlas

Cohort

  • Defines subjects and their arrangement into groups.
  • Different cohorts are needed for different imaging techniques (MRI, fMRI, PET, EEG).
  • Input format: *.xlsx, *.txt ,*.xml, *.atlas
  • Output format: *.mc, *.fc, *.pc, *.ec 

Pre-Analysis

  • Defines connectivity matrix, community structure and sub-graphs (if needed), for analysis.
  • Connectivity matrix is calculated by specifying the type of graph, type of correlation and the management of negative correlation coefficients.
  • Community structure is calculated by specifying the algorithm and parameters used.
  • Different graph analysis are needed for different imaging techniques (MRI, fMRI, PET, EEG).
  • Input format*.xml, *.mc, *.fc, *.pc, *.ec 
  • Output format: *.mga, *.fga, *.pga, *.ega

Analysis

  • Computes global and nodal measures and between-group comparisons and compares the measures with random graphs.
  • The analysis can be done on weighted undirected (WU analysis) and binary undirected graphs by fixing threshold (BUT analysis) or density (BUD analysis).
  • Input format*.xml, *.mga, *.fga, *.pga, *.ega