You need to set the  matlabbatch{1}.spm.spatial.normalise.write.woptions to what you want the output BB and sampling. The default is 2x2x2 and the BB makes it 79x95x79.

If you set them to [NaN NaN NaN; NaN NaN NaN] and [NaN NaN NaN], then it should work.

Best Regards, 

Donald McLaren, PhD

On Mon, May 23, 2016 at 3:20 AM, Alle Meije Wink <a.m.wink@gmail.com> wrote:

Maybe it's better to describe the core problem:

I have an atlas in MNI space (sampled at 1.5 mm)
  /path/to/aal_atlas.nii
and a set of inverse warp parameters to put it in native space of a T1 image: (sampled at 1 mm)
  /path/to/iy_T1.nii

If I call a script that sets
  matlabbatch{1}.spm.spatial.normalise.write.subj(1).def = {'/path/to/iy_T1.nii'};
  matlabbatch{1}.spm.spatial.normalise.write.subj(1).resample = {'/path/to/aal_atlas.nii'};

and then run
  spm_jobman('run',matlabbatch)

my would-be native-space atlas has dimensions 79x95x79 and voxel size 2x2x2 mm.

Neither the bounding box nor the voxel size make sense?
The example scripts I know automatically use the T1's settings - why not now?

Many thanks!