New update fails

[MarcRamos]

Hey I am trying now to start a pipeline with custom parcellation but I get this error:

Exception in thread Thread-4:
Traceback (most recent call last):
File "/usr/lib/python2.7/threading.py", line 551, in __bootstrap_inner
self.run()
File "/usr/local/lib/python2.7/dist-packages/cmp/pipelines/common.py", line 61, in run
if self.stages[stage].has_run():
File "/usr/local/lib/python2.7/dist-packages/cmp/stages/parcellation/parcellation.py", line 136, in has_run
return os.path.exists(self.config.nifti_file)
AttributeError: 'ParcellationConfig' object has no attribute 'nifti_file'

But in the config file there is a nifti_file of the custom parcellation part...

[davidrs06]

Hi Marc,

I think it should work now, can you give it a try ? I've updated our nipype branch also, make sure to download and install the last commit before trying the new version of cmp_nipype.

Thanks a lot !

David

[MarcRamos]

The parcellation error seems to be solved but I've got this now:
Traceback (most recent call last):
File
"/usr/local/lib/python2.7/dist-packages/nipype/pipeline/plugins/multiproc.py",
line 18, in run_node
result['result'] = node.run(updatehash=updatehash)
File "/usr/local/lib/python2.7/dist-packages/nipype/pipeline/engine.py",
line 1391, in run
self._run_interface()
File "/usr/local/lib/python2.7/dist-packages/nipype/pipeline/engine.py",
line 1501, in _run_interface
self._result = self._run_command(execute)
File "/usr/local/lib/python2.7/dist-packages/nipype/pipeline/engine.py",
line 1627, in _run_command
result = self._interface.run()
File "/usr/local/lib/python2.7/dist-packages/nipype/interfaces/base.py",
line 943, in run
self._check_mandatory_inputs()
File "/usr/local/lib/python2.7/dist-packages/nipype/interfaces/base.py",
line 881, in _check_mandatory_inputs
raise ValueError(msg)
ValueError: DataGrabber requires a value for input 'sort_filelist'. For a
list of required inputs, see DataGrabber.help()

What does it mean?

2014-06-03 18:44 GMT+02:00 davidrs06 [email protected]:

Hi Marc,

I think it should work now, can you give it a try ? I've updated our
nipype branch also, make sure to download and install the last commit
before trying the new version of cmp_nipype.

Thanks a lot !

David

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