Hmm, you should be able to:
+ 3dresample the individual volumes to the same "master" grid (-> assuming the "x, y, z" values are still correct in the oddly-gridded dsets):
3dresample -master DSET_ON_GOOD_GRID -prefix OUTPUT -input ODD_GRID_FILE
I don't know if you also want to do this, then, to combine all your masks, but:
if you want to combine all the ROIs into a map where the location of each has a separate integer (assuming they don't overlap):
+ 3dTcat the new volumes into a single 4D dataset:
3dTcat -prefix aaa.nii.gz DSET1 DSET2 DSET3 DSET4 .....
+ Make a mask of where all the nonzero values are across all your dsets (this is not binary, but it will suffice):
3dTstat -abssum -prefix aaa_nonzero.nii.gz aaa.nii.gz
+ and then use 3dTstat again to make a map of the ROIs, where each voxel's value is the index+1 of the volume that is nonzero at that location:
3dTstat -argmax1 -prefix aaa_map_rois.nii.gz -mask aaa_nonzero.nii.gz aaa.nii.gz
That is, once you've concatenated the dsets, each ROI sits in a volume with index "i"; the above command will make a new dset whose value is "i+1" wherever an ROI exists. *If* your ROIs overlap, then this might *not* be the way to go, because you would likely want a better way to select which value gets assigned to a voxel than being later in the concatenated list.
-pt
