The issue is that MATLAB indices start at 1, while AFNI indices start at 0. So when addressing the entire brick with a single index, MATLAB index 372560 is the same voxel as AFNI index 372559, and the MATLAB voxel is at (68, 33, 52) while the AFNI voxel is at (67, 32, 51).
Although it's not the source of your current confusion, another thing to be aware of if you're using software other than AFNI and MATLAB to manipulate your data is that those two programs store the data using the FORTRAN convention, which means that the first index changes fastest as the global index changes. Many other programs use the C convention, in which the
last index changes fastest, and this could cause global indices to disagree across programs.
