Skip to content

ICC: Cannot set the undefined 'sessions_F_map' attribute of a 'ICCOutputSpec' object #2421

Closed
@dangom

Description

@dangom

Summary

Trying to run ICC raises a TraitError with the following description: "TraitError: Cannot set the undefined 'sessions_F_map' attribute of a 'ICCOutputSpec' object."
I may be doing things wrong, in which case a more informative error message would be welcome. Please look at the code snippet under Script/Workflow Details.

Note: I do get maps (icc_map.nii, session_var_map.nii, subject_var_map.nii) as an output in my os.getcwd().

Actual behavior

ICC triggers an exception.

Expected behavior

ICC runs smoothly.

How to replicate the behavior

mkdir /Users/user/test
mv mask.nii.gz sub-{01,02}_ses-{01,02}.nii.gz /Users/user/test
# Where these niftis are sensible "ICC compatible" files
# And now run code pasted below

Script/Workflow details

Please put URL to code or code here (if not too long).

import os.path
from nipype.algorithms import icc

project_dir = '/Users/user/test/'

def fname(sub, ses):
    return os.path.join(project_dir, f'sub-{sub}_ses-{ses}.nii.gz')

lst = [[fname(1, 1), fname(1, 2)], 
       [fname(2, 1), fname(2, 2)]]
mask = os.path.join(project_dir, 'mask.nii.gz')

x = icc.ICC(subjects_sessions=lst, mask=mask)
x.run()

Platform details:

Please paste the output of: python -c "import nipype; print(nipype.get_info()); print(nipype.__version__)"

{'commit_hash': '%h',
 'commit_source': 'archive substitution',
 'networkx_version': '2.0',
 'nibabel_version': '2.2.1',
 'nipype_version': '1.0.0',
 'numpy_version': '1.13.3',
 'pkg_path': '/Users/user/anaconda3/lib/python3.6/site-packages/nipype',
 'scipy_version': '1.0.0',
 'sys_executable': '/Users/user/anaconda3/bin/python',
 'sys_platform': 'darwin',
 'sys_version': '3.6.4 | packaged by conda-forge | (default, Dec 23 2017, 16:54:01) \n[GCC 4.2.1 Compatible Apple LLVM 6.1.0 (clang-602.0.53)]',
 'traits_version': '4.6.0'}

Execution environment

Choose one

  • My python environment outside container

Metadata

Metadata

Assignees

No one assigned

    Labels

    No labels
    No labels

    Type

    No type

    Projects

    No projects

    Milestone

    Relationships

    None yet

    Development

    No branches or pull requests

    Issue actions