# ROI Calculation¶

With a predefined atlas-like ROI file and a descriptive number-label table, the current function can extract mean time series from ROIs and voxels, and calculate Pearson’s correlation as well as its Fisher-z transform. An option is provided to calculate partial correlation between each pair of ROIs, with mean signals of other ROIs as covariates.

**roi file**: ROIs in one nifti file**roi index(*)**: optional. labels of tagged ROIs in a`*.csv`

file. For example:1,SFG 2,MFG 3,IFG

**clustersize thr**: threshold of cluster size.**mask**: could be whole brain mask or gray matter mask.**id index**: identifier to find unique string for each subject**filetype**: files in the filetype will be searched in input directories.**4D nifti files**: if the input data is 4D, check this item. Otherwise uncheck.**input dirs**: directories can be input either using a`*.txt`

file or spm select window.**extract mean**: extract mean time series for each ROI**roi to roi correlation**: calculate correlation between pairs of ROI**roi to whole brain correlation**: calculate correlation between each ROI’s mean time series and voxels in the mask.**Partial correlation**: (check to use Partial correlation, uncheck to use Pearson’s correlation) when calculating correlation, between one roi mean time series and voxels/other time series, the rest of roi mean time serieses will be regressed out from the calculation.**out dir**: output directory for saving results.

**Buttons**:**S**: Save parameters of the current panel to a`*.mat`

file. The`*.mat`

can be further loaded for the panel or be used in a script processing.**L**: Load parameters from`*.mat`

for the current panel.**?**: Help information.