[NiPype] MRIConvert errors

[Dan]

Hi,

I'm running into an issue similar to one I previously had with some of the FSL interfaces. I'm using MRIConvert to convert from NIFTI to Analyze format, but NiPype seems to expect a different output than the one actually produced by the interface:
FileNotFoundError: File/Directory '['/home/ ... /example_func_out001.img']' not found for MRIConvert output 'out_file'.
While the file that is inside the directory is actually called example_func_out.img. I'm not sure if it's a bug or if I'm doing something wrong.

Additionally, I'm getting another error, but unfortunately I don't really have any idea what the source of it is. The error asks me to warn the developers, so here is the stack trace:

120724-11:39:50,69 workflow INFO:
     Traceback (most recent call last):
  File "/usr/local/lib/python2.7/dist-packages/nipype/pipeline/plugins/linear.py", line 37, in run
    node.run(updatehash=updatehash)
  File "/usr/local/lib/python2.7/dist-packages/nipype/pipeline/engine.py", line 1128, in run
    self._run_interface()
  File "/usr/local/lib/python2.7/dist-packages/nipype/pipeline/engine.py", line 1226, in _run_interface
    self._result = self._run_command(execute)
  File "/usr/local/lib/python2.7/dist-packages/nipype/pipeline/engine.py", line 1350, in _run_command
    result = self._interface.run()
  File "/usr/local/lib/python2.7/dist-packages/nipype/interfaces/freesurfer/base.py", line 121, in run
    return super(FSCommand, self).run(**inputs)
  File "/usr/local/lib/python2.7/dist-packages/nipype/interfaces/base.py", line 824, in run
    results.outputs = self.aggregate_outputs(results.runtime)
  File "/usr/local/lib/python2.7/dist-packages/nipype/interfaces/base.py", line 866, in aggregate_outputs
    predicted_outputs = self._list_outputs()
  File "/usr/local/lib/python2.7/dist-packages/nipype/interfaces/freesurfer/preprocess.py", line 398, in _list_outputs
    raise Exception('Not taking frame manipulations into account- please warn the developers')
Exception: Not taking frame manipulations into account- please warn the developers
Interface MRIConvert failed to run.

Thanks,
Dan

[Satrajit Ghosh]

hi dan,

could you please also provide the inputs for the interface/node? i suspect you are doing some frame manipulations and some of those are not supported in the interface.

cheers,

satra

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