diff --git a/nipype/interfaces/fsl/preprocess.py b/nipype/interfaces/fsl/preprocess.py index 3bada9f434..a039484276 100644 --- a/nipype/interfaces/fsl/preprocess.py +++ b/nipype/interfaces/fsl/preprocess.py @@ -678,8 +678,17 @@ def _list_outputs(self): '_variance.ext', cwd=cwd) outputs['std_img'] = self._gen_fname(outputs['out_file'] + '_sigma.ext', cwd=cwd) + + # The mean image created if -stats option is specified ('meanvol') + # is missing the top and bottom slices. Therefore we only expose the + # mean image created by -meanvol option ('mean_reg') which isn't + # corrupted. + # Note that the same problem holds for the std and variance image. + + if isdefined(self.inputs.mean_vol) and self.inputs.mean_vol: outputs['mean_img'] = self._gen_fname(outputs['out_file'] + - '_meanvol.ext', cwd=cwd) + '_mean_reg.ext', cwd=cwd) + if isdefined(self.inputs.save_mats) and self.inputs.save_mats: _, filename = os.path.split(outputs['out_file']) matpathname = os.path.join(cwd, filename + '.mat')