ts_Z_corr not defined #3696
Description
Summary
In NetCorr, there's a check
nipype/nipype/interfaces/afni/preprocess.py
Line 2744 in 237a9a7
AttributeError: 'NetCorrInputSpec' object has no attribute 'ts_Z_corr'if ts_wb_corr is not specified.
- I'm not 100% sure, but I think
ts_Z_corris meant to bets_wb_Zbased on the structure of the check and the definitions of the arguments for 3dNetCorr. - I'm also not sure, but I think the check should check if those values are
Truerather than just if they are defined?
Actual behavior
AttributeError: 'NetCorrInputSpec' object has no attribute 'ts_Z_corr'Expected behavior
-
ts_wb_corrcan be unspecified and interface will be useable.
How to replicate the behavior
- Try to use
nipype.interfaces.afni.preprocess.NetCorrwithoutts_wb_corr
Script/Workflow details
timeseries_correlation = pe.Node(NetCorr(), name=name) if method: timeseries_correlation.inputs.part_corr = method == "Partial" strip_header_node = pe.Node( Function( input_names=["in_file", "out_file"], output_names=["out_file"], imports=["import subprocess"], function=strip_afni_output_header, ), name=f"netcorrStripHeader{method}_{pipe_num}", ) name_output_node = pe.Node( Function( input_names=["atlas_name", "tool", "method"], output_names=["filename"], imports=["import os"], function=connectome_name, ), name=f"connectomeName{method}_{pipe_num}", as_module=True, ) name_output_node.inputs.tool = "Afni" wf.connect( [ ( inputspec, timeseries_correlation, [("in_rois", "in_rois"), ("in_file", "in_file"), ("mask", "mask")], ), ( inputspec, name_output_node, [("atlas_name", "atlas_name"), ("method", "method")], ), ( timeseries_correlation, strip_header_node, [("out_corr_matrix", "in_file")], ), (name_output_node, strip_header_node, [("filename", "out_file")]), (strip_header_node, outputspec, [("out_file", "out_file")]), ] )(FCP-INDI/C-PAC/CPAC/connectome/connectivity_matrix.py#L163-L209@043a004)
Platform details:
{'commit_hash': '<not found>', 'commit_source': '(none found)', 'networkx_version': '3.1', 'nibabel_version': '5.1.0', 'nipype_version': '1.8.6', 'numpy_version': '1.25.1', 'pkg_path': '/usr/share/fsl/6.0/lib/python3.10/site-packages/nipype', 'scipy_version': '1.11.1', 'sys_executable': '/usr/share/fsl/6.0/bin/python', 'sys_platform': 'linux', 'sys_version': '3.10.6 | packaged by conda-forge | (main, Aug 22 2022, ' '20:36:39) [GCC 10.4.0]', 'traits_version': '6.3.2'}Execution environment
Choose one
- My python environment inside container [Base Tag: 🔖
1.8.6]