Defaults
Defaults are specified in icatb_defaults.m file. The following are
the main variables involved in GIFT and EEGIFT:
- Colors
- Colors are RGB values i.e, [0 0 0] means black. Background color
can be changed by changing variable values. The variable names are
listed below for figures and user interface controls:
- Figure background color: BG_COLOR
- User Interface controls except push button background color:
BG2_COLOR
- User Interface controls except push button font color:
FONT_COLOR
- BUTTON_COLOR - Push button background color
- BUTTON_FONT_COLOR - Push button font color
- Fonts for user interface controls
- UI_FONTNAME - font name.
UI_FONTUNITS - font units.
UI_FS - font size.
- Display Defaults
- Display defaults in display GUI can be changed by accessing
defaults like:
- SORT_COMPONENTS: options available are 'No' to 'Yes'.
- IMAGE_VALUES: options available are 'Positive', 'Positive and
Negative', 'Absolute Value' and 'Negative'.
- CONVERT_Z : options are 'Yes' and 'No'.
- THRESHOLD_VALUE : Threshold value to use voxels above or equal
to the threshold
- IMAGES_PER_FIGURE : Options are '1', '4', '9', '16', '25'.
- ANATOMICAL_PLANE: 'axial', 'sagital' and 'coronal'.
- DETRENDNUMBER
- Detrend defaults can be changed by changing the variable
DETRENDNUMBER value. Options are 0, 1, 2 and 3.
- Smoothing parameters
- When SMOOTHPARA variable is changed to 'Yes' the time courses
are smoothed by the value indicated in the variable SMOOTHINGVALUE.
- FLAG_ACKNOWLEDGE_CREATORS:
- FLAG_ACKNOWLEDGE_CREATORS variable used to display
acknowledgement for creators. You can turn off the dialog box by
changing variable to 'off'.
- ICAOPTIONS_WINDOW_DISPLAY:
- ICAOPTIONS_WINDOW_DISPLAY variable used to display ICA options
window. You can turn off the figure window by changing variable to
'off'.
- STORE_DIRECTORY_INFORMATION:
- When STORE_DIRECTORY_INFORMATION variable is changed to 'Yes',
directories specified in cell array DIRS_TO_BE_STORED are stored in
the file selection window.
- ZIP_IMAGE_FILES:
- When this variable is set to 'Yes', the component images will be
compressed to a zip file based on their viewing set.
- METHOD_ENTERING_REGRESSORS:
- Variable has three options like 'AUTOMATIC', 'GUI' and 'BATCH'
for temporal sorting. Each option is explained below:
- 'AUTOMATIC' - Regressors in 'SPM.mat' file will be used directly.
For 'Different regressors over sessions' or 'Different regressors for
subjects and sessions' session related regressors will be used.
- 'GUI' - Figure window will open to select regressors.
- 'BATCH' - Regressors can be entered using a text file by
specifying the file name for variable TXTFILE_REGRESSORS. This is the
best way to enter regressors if you have many data-sets and if you
have selected 'Different regressors over subjects and sessions'.
- FLIP_ANALYZE_IMAGES:
- Flip parameter for the analyze images. Default value is 0.
- NUM_RUNS_GICA:
- Number of times ICA will be run. Default is 1.
- DEFAULT_MASK_OPTION:
- Mask is calculated by doing a Boolean AND of voxels that surpass or equal
the mean. By default first file for each subject is used. You can use all files
by changing variable value to 'all_files'.
- OPEN_DISPLAY_GUI:
- Option is provided to open the display GUI automatically after the
analysis. You can turn off the option by changing variable value to 0.
- CENTER_IMAGES
- A value of 1 means subject spatial maps will be centered based on the peak
of the distribution.
- PREPROC_DEFAULT: Data pre-processing default.
- 1 - Remove mean per time point
- 2 - Remove mean per voxel
- 3 - Intensity normalization
- 4 - Variance normalization
- PCA_DEFAULT - PCA default.
- 1 - Standard
- 2 - Expectation Maximization
- BACKRECON_DEFAULT: Backreconstruction default.
- 1 - Regular
- 2 - Spatial-temporal Regression
- 3 - GICA3
- SCALE_DEFAULT- Scaling components default.
- 0 - No scaling
- 1 - Percent signal change
- 2 - Z-scores