nipy/nipype — pull request #826 by swederik (2014-03-31 16:26:18+00:00)
Title: BF: Added out_file to SPM ApplyTransform

I just tried to use this interface and it didn't seem to apply the manually estimated reorientation matrix correctly.

Took a look at the code and it seemed to be applying an inverted version of the matrix. So I fixed that and just copy/pasted the code from spm_run_reorient.m. Now it will also create a new file with the applied transformation.

Note that you won't be able to actually SEE the proper reorientation until the file is resliced (even to the same resolution it is current at..). I am unsure whether or not we should include that step explicitly in this interface. My current workaround is to use Freesurfer's mri_convert to conform the reoriented file.

Seems better to have it create a new file than dangerously modifying the input file.