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LTS5 / cmp_nipype

This repository is meant to host a beta version for the future release of the ConnectomeMapper.
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New update fails #33

Open MarcRamos opened 10 years ago

MarcRamos commented 10 years ago

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 commented 10 years ago

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 commented 10 years ago

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 notifications@github.com:

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

— Reply to this email directly or view it on GitHub https://github.com/LTS5/cmp_nipype/issues/33#issuecomment-44989703.