The Autoscoper application is designed to work with trials. Only a single trial may be open at one time. New trials may be created manually, or via the File/New Trial (ctrl-N) dialog.
To create a new trial manually, open up a text editor, such as notepad. For each camera in the file enter the text below substituting the italicized text with the correct specifications (see required files and information here). VolumeFlip allows you to flip the axes of your bone model. 1 means flip and 0 means do not flip. x and y correspond to the axis within a single image slice, and z corresponds to the axis across the slices (Default is 0 0 0 meaning no flip).
# Camera 1
mayaCam_csv complete path including file name to mayacam file for camera 1
CameraRootDir complete path to undistorted video frames for camera 1
# Camera 2
mayaCam_csv complete path including file name to mayacam file for camera 2
CameraRootDir complete path to undistorted video frames for camera 2
VolumeFile complete path including file name to tif file containing bone volume
VoxelSize in plane x in mm in plane y in mm slice thickness in mm
VolumeFlip x y z
Once you have entered all of this information, save the text file. Use File/Open menu command to open and work with this trial in the Autoscoper.