As far as I understand you get a 3D logical array from a program. This is not a valid "binary image" for the used function. The solution seems to be trivial: If you get an input, which cannot be used as input of your function, don't use it as input to your function. Either run the other program such, that you get a logical 2D matrix, or convert the data (perhaps: any(img, 3) ) such, that you get the required dimensions.
If you want a more specific suggestion, explain, which program creates the unusual array and what you have tried to fix this.
