Setup ICA Analysis


Before entering the parameters using Setup ICA, figure out how many data-sets you are analyzing. Use batch script to run the analysis or entering design matrix (required during temporal sorting) for large data-sets.

Setup ICA Analysis step involves entering parameters for the group ICA analysis. When you click Setup ICA Analysis button, a figure window will open to select the analysis output directory. After the directory is selected, parameter options figure (Figure 1) will be displayed. The parameters in the figure will be explained step by step and for additional information click on the link highlighted. Some of the user interface controls are shielded from the user. These controls will be shown when you click SetupICA-Defaults menu.

Figure 1: Initial Parameter Select Window

Main User Interface Controls:

Enter name (Prefix) of Output Files
Prefix string to all the output files created by the GIFT.
Have You Selected The fMRI Data Files?
Select
Yes
Do you want to estimate the number of independent components?
Yes
Number of IC
Number of independent components extracted from the data.
Do You Want to Autofill Data Reduction Values?
Numbers for principal components are auto-filled. You can take a look at these parameters by clicking on "Setup ICA-Defaults" menu.
Which algorithm do you want to use?
ICA algorithms like Infomax, FastICA, Erica, Simbec, JADE OPAC, Evd, Amuse, SDD ICA, Semi-blind ICA, Constrained ICA (Spatial), Radical ICA , Combi, ICA-EBM and FBSS are incorporated.
Note: ICA options window (Figure 2) will popup depending on the algorithm selected. Presently, ICA options are available for Infomax, FastICA, SDD ICA, Semi-blind ICA and Constrained ICA (Spatial) . ICA options window can be turned off by replacing variable ICAOPTIONS_WINDOW_DISPLAY to 'off' (Defaults).
Which Group ICA Analysis You Want To Use?
Options are 'Regular' and 'ICASSO'. When you select 'ICASSO', ICA is run several times and the best estimate for each component is used.

Figure 2: ICA Options Window

Figure 3: Completed Parameter Select Window

Figure 3 shows the completed parameters. Press Done button once the answers for the parameters are entered. Parameter file for the analysis is created in the working directory with the suffix '_ica_parameter_info.mat'

After the parameters are saved in a file, use Run Analysis button to run the analysis.