resampleToPixdims and resampleToReference

package). Refactored, cleaned up, and enhanced to accept an arbitrary affine
transform - can be used to resample an image into any other space.

alignemnt of the input and resampled images to be adjusted.

this is all handled by nibabel. Also never keeps its own ref to file object.
Image.save always saves to a temp file, then moves that to the destination -
avoid any problems with mmap/indexed_gzip.

get image data as numpy array.

state. Image.save ensures that file name has an extension. MGHImage uses both
of these changes so that its initial save state is accurate, and when it
is saved, it is saved as a nifti

DicomImage

class.

might be in memory.

doc tweaks.

related code in atlas classes

has no effect when downsampling to a new shape where voxel centres are
aligned.

for us when a new nibabel image is created from an array+existing header

the former aligns on the centre of voxel (0, 0, 0), whereas the latter aligns
on the corner.

adjusted resample method to force float output (although this might change).