nipy / nipype

Workflows and interfaces for neuroimaging packages
https://nipype.readthedocs.org/en/latest/
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global name 'b0_indices' is not defined #1232

Closed vsaase closed 8 years ago

vsaase commented 8 years ago

Hi, I'm new to nipype, this happens when I try to run the following code:

from os.path import abspath
from nipype.workflows.dmri.fsl.artifacts import all_fmb_pipeline

allcorr = all_fmb_pipeline()
allcorr.inputs.inputnode.in_file = abspath('Pres2.nii.gz')
allcorr.inputs.inputnode.in_bval = abspath('Pres2.bval')
allcorr.inputs.inputnode.in_bvec = abspath('Pres2.bvec')
allcorr.inputs.inputnode.bmap_mag = abspath('Pres2_grefieldmappings010a1001.nii.gz')
allcorr.inputs.inputnode.bmap_pha = abspath('Pres2_grefieldmappings011a2001.nii.gz')
allcorr.inputs.inputnode.epi_param = abspath('epi_param.txt')
allcorr.run()

https://gist.github.com/vsaase/436b47f2eb8652446853#file-crash-20151003-165858-brain-b0_avg-pklz

output from nipype.get_info():

{'commit_hash': 'f9c98ba',
 'commit_source': 'archive substitution',
 'networkx_version': '1.9',
 'nibabel_version': '2.0.1',
 'numpy_version': '1.8.2',
 'pkg_path': '/usr/lib/python2.7/dist-packages/nipype',
 'scipy_version': '0.14.0',
 'sys_executable': '/usr/bin/python',
 'sys_platform': 'linux2',
 'sys_version': '2.7.9 (default, Mar  1 2015, 12:57:24) \n[GCC 4.9.2]',
 'traits_version': '4.4.0'}
oesteban commented 8 years ago

Thanks for reporting, I take on this.