CPAC WEB Pipeline BUilder Errors

Joshua_Lee · September 30, 2022, 7:06pm

CPAC WEB Pipeline BUilder Errors, mostly comes down to a missing key and strings instead of floats. I don’t know the appropriate github to report bugs in the builder utility:

Traceback (most recent call last):
File “/code/run.py”, line 807, in
run_main()
File “/code/run.py”, line 499, in run_main
c = Configuration(c)
File “/code/CPAC/utils/configuration.py”, line 134, in init
config_map = schema(config_map)
File “/code/CPAC/pipeline/schema.py”, line 1092, in schema
return latest_schema(_changes_1_8_0_to_1_8_1(config_dict))
File “/usr/local/miniconda/lib/python3.7/site-packages/voluptuous/schema_builder.py”, line 272, in call
return self._compiled([], data)
File “/usr/local/miniconda/lib/python3.7/site-packages/voluptuous/schema_builder.py”, line 595, in validate_dict
return base_validate(path, iteritems(data), out)
File “/usr/local/miniconda/lib/python3.7/site-packages/voluptuous/schema_builder.py”, line 433, in validate_mapping
raise er.MultipleInvalid(errors)
voluptuous.error.MultipleInvalid: expected float for dictionary value @ data[‘pipeline_setup’][‘system_config’][‘maximum_memory_per_participant’]

Traceback (most recent call last):
File “/code/run.py”, line 807, in
run_main()
File “/code/run.py”, line 499, in run_main
c = Configuration(c)
File “/code/CPAC/utils/configuration.py”, line 134, in init
config_map = schema(config_map)
File “/code/CPAC/pipeline/schema.py”, line 1092, in schema
return latest_schema(_changes_1_8_0_to_1_8_1(config_dict))
File “/usr/local/miniconda/lib/python3.7/site-packages/voluptuous/schema_builder.py”, line 272, in call
return self._compiled([], data)
File “/usr/local/miniconda/lib/python3.7/site-packages/voluptuous/schema_builder.py”, line 595, in validate_dict
return base_validate(path, iteritems(data), out)
File “/usr/local/miniconda/lib/python3.7/site-packages/voluptuous/schema_builder.py”, line 433, in validate_mapping
raise er.MultipleInvalid(errors)
voluptuous.error.MultipleInvalid: expected int for dictionary value @ data[‘pipeline_setup’][‘system_config’][‘max_cores_per_participant’]

Traceback (most recent call last):
File “/code/run.py”, line 807, in
run_main()
File “/code/run.py”, line 499, in run_main
c = Configuration(c)
File “/code/CPAC/utils/configuration.py”, line 134, in init
config_map = schema(config_map)
File “/code/CPAC/pipeline/schema.py”, line 1092, in schema
return latest_schema(_changes_1_8_0_to_1_8_1(config_dict))
File “/usr/local/miniconda/lib/python3.7/site-packages/voluptuous/schema_builder.py”, line 272, in call
return self._compiled([], data)
File “/usr/local/miniconda/lib/python3.7/site-packages/voluptuous/schema_builder.py”, line 595, in validate_dict
return base_validate(path, iteritems(data), out)
File “/usr/local/miniconda/lib/python3.7/site-packages/voluptuous/schema_builder.py”, line 433, in validate_mapping
raise er.MultipleInvalid(errors)
voluptuous.error.MultipleInvalid: expected int for dictionary value @ data[‘pipeline_setup’][‘system_config’][‘num_OMP_threads’]

Traceback (most recent call last):
File “/code/run.py”, line 807, in
run_main()
File “/code/run.py”, line 499, in run_main
c = Configuration(c)
File “/code/CPAC/utils/configuration.py”, line 134, in init
config_map = schema(config_map)
File “/code/CPAC/pipeline/schema.py”, line 1092, in schema
return latest_schema(_changes_1_8_0_to_1_8_1(config_dict))
File “/usr/local/miniconda/lib/python3.7/site-packages/voluptuous/schema_builder.py”, line 272, in call
return self._compiled([], data)
File “/usr/local/miniconda/lib/python3.7/site-packages/voluptuous/schema_builder.py”, line 595, in validate_dict
return base_validate(path, iteritems(data), out)
File “/usr/local/miniconda/lib/python3.7/site-packages/voluptuous/schema_builder.py”, line 433, in validate_mapping
raise er.MultipleInvalid(errors)
voluptuous.error.MultipleInvalid: expected float for dictionary value @ data[‘nuisance_corrections’][‘2-nuisance_regression’][‘Regressors’][0][‘Censor’][‘thresholds’][0][‘value’]

Traceback (most recent call last):
File “/code/run.py”, line 807, in
run_main()
File “/code/run.py”, line 499, in run_main
c = Configuration(c)
File “/code/CPAC/utils/configuration.py”, line 134, in init
config_map = schema(config_map)
File “/code/CPAC/pipeline/schema.py”, line 1092, in schema
return latest_schema(_changes_1_8_0_to_1_8_1(config_dict))
File “/usr/local/miniconda/lib/python3.7/site-packages/voluptuous/schema_builder.py”, line 272, in call
return self._compiled([], data)
File “/usr/local/miniconda/lib/python3.7/site-packages/voluptuous/schema_builder.py”, line 595, in validate_dict
return base_validate(path, iteritems(data), out)
File “/usr/local/miniconda/lib/python3.7/site-packages/voluptuous/schema_builder.py”, line 433, in validate_mapping
raise er.MultipleInvalid(errors)
voluptuous.error.MultipleInvalid:

‘tse_roi_paths’ takes a dictionary with paths to region-of-interest (ROI)
NIFTI files (.nii or .nii.gz) as keys and a comma separated string
of analyses to run. For example, if you wish to run Avg and
MultReg, you would enter:

'/path/to/ROI.nii.gz': Avg, MultReg

Available analyses for ‘tse_roi_paths’ are {‘SpatialReg’, ‘Voxel’, ‘Avg’}

for dictionary value @ data[‘timeseries_extraction’][‘tse_roi_paths’]

File “/code/run.py”, line 807, in
run_main()
File “/code/run.py”, line 788, in run_main
test_config=(1 if args.analysis_level == “test_config” else 0)
File “/code/CPAC/pipeline/cpac_runner.py”, line 583, in run
raise e
File “/code/CPAC/pipeline/cpac_runner.py”, line 580, in run
p_name, plugin, plugin_args, test_config)
File “/code/CPAC/pipeline/cpac_pipeline.py”, line 443, in run_workflow
subject_id, sub_dict, c, p_name, num_ants_cores
File “/code/CPAC/pipeline/cpac_pipeline.py”, line 1376, in build_workflow
wf = connect_pipeline(wf, cfg, rpool, pipeline_blocks)
File “/code/CPAC/pipeline/cpac_pipeline.py”, line 1064, in connect_pipeline
wf = nb.connect_block(wf, cfg, rpool)
File “/code/CPAC/pipeline/engine.py”, line 1277, in connect_block
pipe_x, opt)
File “/code/CPAC/nuisance/nuisance.py”, line 2326, in nuisance_regression
nuis = create_nuisance_regression_workflow(opt, name=‘nuisance_regression’
File “/code/CPAC/nuisance/nuisance.py”, line 1520, in create_nuisance_regression_workflow
censor_methods))
ValueError: Improper censoring method specified (None), should be one of [‘Kill’, ‘Zero’, ‘Interpolate’, ‘SpikeRegression’].

amygutierrez · October 3, 2022, 7:01pm

Hi! I’ll be happy to take a look at this. Can you send me some more information, like the docker or singularity command you used to run it (i.e. docker run …) and the pipeline config if possible?

Joshua_Lee · October 8, 2022, 5:58pm

cpac 1.8.4 docker.
i do not have the command or config file anymore. I generated the config using the website utility. The above errors relate to either using strings when cpac expects floats, and a missing method parameter (kill) for the censoring. Manual correction fixed this issue in the config file.

amygutierrez · October 11, 2022, 6:20pm

Oh okay, thank you for the explanation! For the missing method parameter, did you set it as ‘Kill’ using the website utility, but when the YML was generated, it was blank?