Release Notes Causality Analysis Toolbox V0.3 (Last update: 25/07/13)

The main modifications applied to this version of the toolbox, as compared
to the previous released version V0.2, are listed below:

(1) The "MAIN.m" script from which the toolbox runs (as described in the User's
guide document) has been transformed into the function "MAIN(ParamFile)".

So, for the automatic run-mode, the user needs to pre-define the parameter file
to be used: ParamFile = '.../.. .mat' and call the function MAIN(ParamFile).
For the interactive mode, no ParamFile is predefined and the user calls the
main function simply as MAIN(). He is further asked to specify one-by-one the
needed parameters through the command window (as explained in the user's guide
document).

(2) The "visualize_causality.m" script that the user needs to run, in order to
visualize the causality results, has been modified, such that:

The user can define the input ROIs datafile and the Causality results file
through two popup windows. No intervention/modification in the script is required.
In this version a default head model is loaded in the script (no user input is
asked for this), as the head anatomy is not further used in the currently supported
visualization (causality analysis at source level / visualization on the cortex).
The brain anatomy is defined in the structure ROITS -> field ROITS.cortex (Input
data file) so no additional input "anat.mat" is required to be specified by the user.

(3) The file "ROITS_cortex_BS_2_eConnectome_adaptation_guidelines.txt" has been added
in the /Documentation subfolder of the toolbox root directory. This file contains guidelines
for:

the required transformation to be applied to a BrainStorm brain anatomy, such that it
is compatible with the eConnectome causality visualization that is integrated in
this toolbox
the definition of the ROIs'vertices based on a "Scouts.mat" structure, extracted from
BrainStorm.

(4) The variable "Causality_temp" has beed added in the output Causality_results .mat file.
This variable is a structure with 2 fields:

Causality_temp.gc : the time-domain conditional Granger Causality
Causality_temp.pgc : the time-domain partial Granger Causality

Surrogate distributions for these two causality measures are accordingly saved in the
Surrogate_pdfs structure. These are the:

Surrogate_pdfs.gc_temp and Surrogate_pdfs.pgc_temp.

The results of the significant thresholding are saved in the additional fields:

PR_tab.PR_gc_temp and PR_tab.PR_pgc_temp
ST_tab.st_gc_temp and ST_tab.st_pgc_temp

No visualization of the two new causality meausures is supported in the current version of
the toolbox. The computed values are only made available for further exploitation/visualization
using external tools.

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