If the data was acquired in the 'usual' MNI way:

x increases from px left to right, 20 slices, 8 mm step size
z increases from px inferior to superior, 256 slices, -1 mm step size
y increases from px posterior to anterior, 256 slices, -1 mm step size

Then for each T2/PD volume run mincreshape:

mincreshape -dimrange echo_time=0 subject_file_run_number_etc.mnc
subject_file_run_number_pd.mnc

mincreshape -dimrange echo_time=1 subject_file_run_number_etc.mnc
subject_file_run_number_t2.mnc

After the interleaved volumes have been separated, create a {pd|t2}
volume with:

concat_mri subject_file_*_{pd|t2}.mnc subject_file_{pd|t2}.mnc