# ROI Mapping¶

When visualizing ROIs from an atlas or clusters from a user-defined 3D volume (e.g., clusters with significant difference between sample means), we can use the current function to extract and shade the surface of each number-tagged ROI/cluster in random or user defined colors. The ROIs/clusters of the input 3D image should be tagged with positive-integers. With an additional input of a reference *.csv table containing number-label pairs (as described in Utilities -> DICOM Convert), we can further parse the labels of each shaded ROI/cluster and present them in a legend.

• alpha: degree of transparency.

• display: mode of display.

• display surface: show surface.

• surface: surface file.

• display legend: display legend.

• roi file: extract mean intensity in the roi tagged by numbers.

• roi info*: optional. two columns of information for each labeled cluster in a *.csv file. For example:

1,SFG
2,MFG
3,IFG

• roi vals: select which roi to display.

• color: optional. use random color or input color file.

• color file: the input color could be (ROI tag, R, G, B):

1,255,155,100
2,1,1,1

• output color: output color of current image.

• 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.