When you run it can you see if it creates a log file?  Does it create a folder called intermediate processing? 
This is where DKE will try and find your images : dir_subj = fullfile(studydir, subject_list{isubject}); % subject root folder
I also think this is where it is trying to find your reco file. So you might have to put that in the same folder as 2dseq. 

Does that work? Sorry it's been a while since I used Bruker data :) 

Emilie