I open the registered image using test1 and test2, but the menu of 3D image atlas is not active.
Then i try this,but it doesnot work
command:
./brainaligner_linux_redhat_fedora_64bit -t test1_256.tif -s test2_256.tif  -L test1_256.marker, -C 1, -c 2, -w 10, -H 2, -j 1, -i 2, -B 1024,  -o t21_256.tif

Then i get:

The current input file has the surfix [tif]
#original slice=108 original rez=1.00000 -> #output slices=108 new rez=1.00000
The current input file has the surfix [tif]
#original slice=108 original rez=1.00000 -> #output slices=108 new rez=1.00000
After preprocessing:
 Size of subject_image = [256 256 108 1], size of target_image = [256 256 108 1].
The reference channelNo of either subject image or target image is (or both are) invalid (bigger than the number of channels the images have). Exit.