You can create an empty 3D Occupancy map using the occupancyMap3D function. Then, you can use the setOccupancy object function to specify whether a given location is free or is an obstacle, using the 3D matrix you have. The syntax for this function is:
Here, map3D is the 3D Occupancy map that you have created. xyz is a matrix in which each row is a 1-by-3 vector corresponding to the indices of the elements in your 3D matrix. occval is a column vector in which each element corresponds to the value of the element at that index position, that is, either zero or one.
Finally, you can display the map using the show object function.
For an example on how to use the obtained map to plan the path, refer to the following example:
Hope this helps!