nipype

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Summary

Bug reports on nipype workflows are becoming essentially useless, as the exceptions now wrap around the original exceptions and we get very little traceback information. Further, the crashfiles that are emitted merely show the same exception and no terminal output that would help diagnose.

A good example of this is https://github.com/nipreps/smriprep/issues/286, where we had to provide users with explicit debugging steps. Below I paste a successful _report/report.rst, which also shows nothing. This is a significant regression.

Node: fsl
=========


 Hierarchy : _applyxfm_roi18
 Exec ID : _applyxfm_roi18


Original Inputs
---------------


* angle_rep : <undefined>
* apply_isoxfm : <undefined>
* apply_xfm : True
* args : <undefined>
* bbrslope : <undefined>
* bbrtype : <undefined>
* bgvalue : <undefined>
* bins : <undefined>
* coarse_search : <undefined>
* cost : <undefined>
* cost_func : <undefined>
* datatype : <undefined>
* display_init : <undefined>
* dof : <undefined>
* echospacing : <undefined>
* environ : {'FSLOUTPUTTYPE': 'NIFTI_GZ'}
* fieldmap : <undefined>
* fieldmapmask : <undefined>
* fine_search : <undefined>
* force_scaling : <undefined>
* in_file : /scratch/nibabies_21_1_wf/single_subject_470437_1mo_wf/func_preproc_ses_1mo_task_rest_acq_AP_run_02_wf/bold_std_trans_wf/_std_target_MNIInfantcohort-1.cohort1/merge/vol0000_xform-00000_merged.nii.gz
* in_matrix_file : /scratch/nibabies_21_1_wf/single_subject_470437_1mo_wf/func_preproc_ses_1mo_task_rest_acq_AP_run_02_wf/subcortical_mni_alignment_wf/roi2atlas/mapflow/_roi2atlas18/vol0018_flirt.mat
* in_weight : <undefined>
* interp : spline
* min_sampling : <undefined>
* no_clamp : <undefined>
* no_resample : <undefined>
* no_resample_blur : <undefined>
* no_search : <undefined>
* out_file : <undefined>
* out_log : <undefined>
* out_matrix_file : <undefined>
* output_type : NIFTI_GZ
* padding_size : <undefined>
* pedir : <undefined>
* ref_weight : <undefined>
* reference : /scratch/nibabies_21_1_wf/single_subject_470437_1mo_wf/func_preproc_ses_1mo_task_rest_acq_AP_run_02_wf/subcortical_mni_alignment_wf/split_atlas_rois/vol0018.nii.gz
* rigid2D : <undefined>
* save_log : <undefined>
* schedule : <undefined>
* searchr_x : <undefined>
* searchr_y : <undefined>
* searchr_z : <undefined>
* sinc_width : <undefined>
* sinc_window : <undefined>
* uses_qform : <undefined>
* verbose : <undefined>
* wm_seg : <undefined>
* wmcoords : <undefined>
* wmnorms : <undefined>


Execution Inputs
----------------


* angle_rep : <undefined>
* apply_isoxfm : <undefined>
* apply_xfm : True
* args : <undefined>
* bbrslope : <undefined>
* bbrtype : <undefined>
* bgvalue : <undefined>
* bins : <undefined>
* coarse_search : <undefined>
* cost : <undefined>
* cost_func : <undefined>
* datatype : <undefined>
* display_init : <undefined>
* dof : <undefined>
* echospacing : <undefined>
* environ : {'FSLOUTPUTTYPE': 'NIFTI_GZ'}
* fieldmap : <undefined>
* fieldmapmask : <undefined>
* fine_search : <undefined>
* force_scaling : <undefined>
* in_file : /scratch/nibabies_21_1_wf/single_subject_470437_1mo_wf/func_preproc_ses_1mo_task_rest_acq_AP_run_02_wf/bold_std_trans_wf/_std_target_MNIInfantcohort-1.cohort1/merge/vol0000_xform-00000_merged.nii.gz
* in_matrix_file : /scratch/nibabies_21_1_wf/single_subject_470437_1mo_wf/func_preproc_ses_1mo_task_rest_acq_AP_run_02_wf/subcortical_mni_alignment_wf/roi2atlas/mapflow/_roi2atlas18/vol0018_flirt.mat
* in_weight : <undefined>
* interp : spline
* min_sampling : <undefined>
* no_clamp : <undefined>
* no_resample : <undefined>
* no_resample_blur : <undefined>
* no_search : <undefined>
* out_file : <undefined>
* out_log : <undefined>
* out_matrix_file : <undefined>
* output_type : NIFTI_GZ
* padding_size : <undefined>
* pedir : <undefined>
* ref_weight : <undefined>
* reference : /scratch/nibabies_21_1_wf/single_subject_470437_1mo_wf/func_preproc_ses_1mo_task_rest_acq_AP_run_02_wf/subcortical_mni_alignment_wf/split_atlas_rois/vol0018.nii.gz
* rigid2D : <undefined>
* save_log : <undefined>
* schedule : <undefined>
* searchr_x : <undefined>
* searchr_y : <undefined>
* searchr_z : <undefined>
* sinc_width : <undefined>
* sinc_window : <undefined>
* uses_qform : <undefined>
* verbose : <undefined>
* wm_seg : <undefined>
* wmcoords : <undefined>
* wmnorms : <undefined>


Execution Outputs
-----------------


* out_file : /scratch/nibabies_21_1_wf/single_subject_470437_1mo_wf/func_preproc_ses_1mo_task_rest_acq_AP_run_02_wf/subcortical_mni_alignment_wf/applyxfm_roi/mapflow/_applyxfm_roi18/vol0000_xform-00000_merged_flirt.nii.gz
* out_log : <undefined>
* out_matrix_file : <undefined>


Runtime info
------------


* cmdline : flirt -in /scratch/nibabies_21_1_wf/single_subject_470437_1mo_wf/func_preproc_ses_1mo_task_rest_acq_AP_run_02_wf/bold_std_trans_wf/_std_target_MNIInfantcohort-1.cohort1/merge/vol0000_xform-00000_merged.nii.gz -ref /scratch/nibabies_21_1_wf/single_subject_470437_1mo_wf/func_preproc_ses_1mo_task_rest_acq_AP_run_02_wf/subcortical_mni_alignment_wf/split_atlas_rois/vol0018.nii.gz -out vol0000_xform-00000_merged_flirt.nii.gz -omat vol0000_xform-00000_merged_flirt.mat -applyxfm -init /scratch/nibabies_21_1_wf/single_subject_470437_1mo_wf/func_preproc_ses_1mo_task_rest_acq_AP_run_02_wf/subcortical_mni_alignment_wf/roi2atlas/mapflow/_roi2atlas18/vol0018_flirt.mat -interp spline
* duration : 745.396369
* hostname : f16b9a0dcf1f
* prev_wd : /tmp
* working_dir : /scratch/nibabies_21_1_wf/single_subject_470437_1mo_wf/func_preproc_ses_1mo_task_rest_acq_AP_run_02_wf/subcortical_mni_alignment_wf/applyxfm_roi/mapflow/_applyxfm_roi18


Terminal output
~~~~~~~~~~~~~~~


 


Terminal - standard output
~~~~~~~~~~~~~~~~~~~~~~~~~~


 


Terminal - standard error
~~~~~~~~~~~~~~~~~~~~~~~~~


 


Environment
~~~~~~~~~~~


* AFNI_DIR : /opt/afni
* AFNI_IMSAVE_WARNINGS : NO
* AFNI_PLUGINPATH : /opt/afni-latest
* ANTSPATH : /usr/lib/ants
* ANTS_RANDOM_SEED : 64899
* AROMA_VERSION : 0.4.5
* C3DPATH : /opt/convert3d-1.0.0
* CONDA_PYTHON : /opt/conda/bin/python
* CPATH : /opt/conda/include:
* DEBIAN_FRONTEND : noninteractive
* DOCKER_VERSION_8395080871 : 20.10.17
* FREESURFER_HOME : /opt/freesurfer
* FSLDIR : /opt/fsl
* FSLGECUDAQ : cuda.q
* FSLLOCKDIR : 
* FSLMACHINELIST : 
* FSLMULTIFILEQUIT : TRUE
* FSLOUTPUTTYPE : NIFTI_GZ
* FSLREMOTECALL : 
* FSL_DIR : /opt/fsl
* FS_LICENSE : /opt/freesurfer/license.txt
* FUNCTIONALS_DIR : /opt/freesurfer/sessions
* HOME : /home/nibabies
* HOSTNAME : f16b9a0dcf1f
* IS_DOCKER_8395080871 : 1
* KMP_DUPLICATE_LIB_OK : True
* KMP_INIT_AT_FORK : FALSE
* LANG : en_US.UTF-8
* LC_ALL : en_US.UTF-8
* LD_LIBRARY_PATH : /opt/fsl/lib:
* LOCAL_DIR : /opt/freesurfer/local
* MINC_BIN_DIR : /opt/freesurfer/mni/bin
* MINC_LIB_DIR : /opt/freesurfer/mni/lib
* MKL_NUM_THREADS : 1
* MNI_DATAPATH : /opt/freesurfer/mni/data
* MNI_DIR : /opt/freesurfer/mni
* MNI_PERL5LIB : /opt/freesurfer/mni/lib/perl5/5.8.5
* NIPYPE_NO_ET : 1
* NO_ET : 1
* OMP_NUM_THREADS : 1
* PATH : /opt/conda/bin:/opt/ICA-AROMA:/opt/freesurfer/bin:/opt/freesurfer/tktools:/opt/freesurfer/mni/bin:/opt/fsl/bin:/opt/convert3d-1.0.0/bin:/opt/afni-latest:/usr/lib/ants:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
* PERL5LIB : /opt/freesurfer/mni/lib/perl5/5.8.5
* PYTHONNOUSERSITE : 1
* PYTHONWARNINGS : ignore
* SUBJECTS_DIR : /opt/freesurfer/subjects
* TERM : xterm

This is recent nipype (>=1.7, I think).