RF: use nipy save to save image

Avoid hacking with affine by saving with `nipy.save_image`.

nipy/algorithms/registration/scripting.py

@@ -22,6 +22,7 @@
 
 from .groupwise_registration import SpaceTimeRealign
 import nipy.algorithms.slicetiming as st
+from nipy.io.api import save_image
 
 timefuncs = st.timefuncs.SLICETIME_FUNCTIONS
 
@@ -159,12 +160,6 @@ def space_time_realign(input, tr, slice_order='descending', slice_dim=2,
     if apply:
         new_reggy = reggy.resample(align_runs=True)
         for run_idx, new_im in enumerate(new_reggy):
-            new_data = new_im.get_data()
-            # We use the top 4 by 4 as the affine for the new file we will
-            # create:
-            new_aff = new_im.affine[:4, :4]
-            new_aff[:, 3] = new_im.affine[:4, 4]
-            new_ni = nib.Nifti1Image(new_data, new_aff)
             # Save it out to a '.nii.gz' file:
             old_fname_split = op.split(fnames[run_idx])
             # We retain the file-name adding '_mc' regardless of where it's
@@ -174,7 +169,7 @@ def space_time_realign(input, tr, slice_order='descending', slice_dim=2,
                 new_path = old_fname_split[0]
             else:
                 new_path = out_name
-            new_ni.to_filename(op.join(new_path, new_fname))
+            save_image(new_im, op.join(new_path, new_fname))
 
     if make_figure:
         figure, ax = plt.subplots(2)