Hi Ekaterina,
okay, good, but now I'm in a quandary - you listed resp_mean_mni.nii in the list of files inside pestica_afni_v1_2, but 3dAllineate cannot load it.  Can you post the output of "ls -l resp_mean_mni.nii" from your pestica directory?  It should be a softlink to a file that does exist (most likely pestica_volumes/resp_pestica_16mm3_avg_mni.nii).  I see you have a couple of other files in there - I recommend you don't run any PESTICA tools from within the PESTICA directory, but instead make a new directory somewhere else in your filesystem with the example data moved there.

erik