you can use the GUI batch function to prepare a batch with the Dartel functions (batchmenu -> spm, tools, dartel tools), set the necessary dependencies and leave information about e.g. scan location blank. Then you can use "save batch and script" to create two m-files (batchname.m and batchname_job.m) which contain all the information. 

Then just loop through the subject folders by adapting the first m-file (filling in the information about the scans you left blank earlier) and running the script.

hope this help

david