* trying to incorporate an automatic mask resampling strategy. The idea is that when you resample a file that is associated with a file handler, you want to resample the mask as well. So instead of calling the mincresample minc atom, you can now call the mincresampleFileAndMask minc atom. This module will do the same as mincresample, but will also check the presence of a mask associated with the file handler. If that mask exists, the mask will be resampled using the same transform as the main file. One thing to keep in mind is that (at the moment) none of these files are set as last base volume by default. You still need to take care of this yourself. For improved user friendliness (and fewer chances of mistakes/omissions) we should look into a way to set all this automatically.

* change in the main mincresample minc atom: the argArray argument can be used to add options to mincresample that would be difficult to handle in any other way. It simply holds a list of arguments to be used for the final command. Up till now, the actual comnmand line command (mincresample) was added to this argArray if it was provided to the atom. However, this altered the input argument. In the new function mincresampleFileAndMask, this argArray is possibly used twice (to resample the main file and potentially the mask), and the argArray might have to be used twice. Having this array change within the mincresample atom caused some issues. Now this parameter is left unaltered by the mincresample minc atom.