I am having the following problem after update the brainstorm. Please let me know a solution
MATLAB\brainstorm3\external\ImaGIN\anat
MATLAB\brainstorm3\external\ImaGIN\math
This is because you added permanently the Brainstorm subfolders to your Matlab path. And some of these subfolders were removed from the distribution.
As indicated in the installation instructions, do not add Brainstorm subfolders in your path: http://neuroimage.usc.edu/brainstorm/Installation#Start_Brainstorm