coefficient fields

between fsl.transform.nonlinear and fsl.data.image.

coefficient field to displacement field. Check for TOPUP intent codes

are fine. Generating a slightly less incorrect (but still incorrect) v2w
affine for the former. Bug in test script

intent code to be changed. Nifti class emits new "header" notifier topic
when intent changes.

read/write routines

be useful outside of the Nifti class (for testing, at least)

fsl, and world coordinate systems. New getAffine method allows you to get an
affine between any of the coordinate systems

a file name. Bitmap.asImage passes dataSource through to Image.__init__

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