Reorient2Std failure when processing correctly oriented image with different output type

[lebedov]

I've noticed that if one attempts to run fslreorient2std on a nifti file that doesn't need to be reoriented but with an output file type that differs from that of the input (e.g., fslreorient2std input.nii output.nii.gz or fslreorient2std input.nii.gz output.nii), the output file will always be of the same type as the input regardless of what one specifies on the command line and regardless of the value of the FSLOUTPUTTYPE env variable. This behavior can cause Reorient2Std to fail if it is fed an nii.gz file that doesn't need to be reoriented as input and the output type is assumed to also be nii.gz. The class should check the actual generated output and compress it with gzip if it isn't already compressed and the output type is NIFTI_GZ.

I'm using FSL 5.0.9 built on Ubuntu 14.04.4 with Python 2.7.12 and nipype 0.12.1.

[satra]

@lebedov - is this an fsl issue that we should check for in nipype? has this been reported to FSL?

[lebedov]

I suspect that it is unintended behavior, but I'm waiting to hear back from the FSL folks to confirm - discussion thread here.

[lebedov]

Quick-and-dirty workaround posted here - probably should use nipype.interfaces.base.run_command rather than calling os.system directly to run gzip/gunzip if deemed appropriate for incorporation into the Reorient2Std class.

[lebedov]

Folks on the FSL list confirmed the behavior I reported, although it still isn't clear whether the behavior was intended or not.