When I run FEATQuery (under cygwin) using a mask file created in FSLView, it fails to run. Two text files are created in the FEATQuery directory. One is empty. The other contains only the following text:
   
Processing FEAT directory 1 : C:/cygwin/home/lipton/data/20040624eppie/FEAT/fmrib.feat
Error - mask size doesn't match any of the images in the FEAT directory
 
I ran avwhd to be sure the mask has the same dimensions as my filtered_func_data. It does. I also made sure that both the .hdr and .img portions of my mask are in the FEAT directory. I can open the same mask in FSLView without any problem.
 
Any help will be much appreciated,
 
Thanks,
 
Michael