How to use the clinica.utils.ux.print_crash_files_and_exit function in clinica
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aramis-lab / clinica / clinica / pipelines / t1_volume_dartel2mni / t1_volume_dartel2mni_cli.py View on Github 
# 'bounding_box': None,
'voxel_size': tuple(args.voxel_size) if args.voxel_size is not None else None,
'modulation': args.modulate,
'fwhm': args.smooth
})
if args.n_procs:
exec_pipeline = pipeline.run(plugin='MultiProc',
plugin_args={'n_procs': args.n_procs})
else:
exec_pipeline = pipeline.run()
if isinstance(exec_pipeline, Graph):
print_end_pipeline(self.name, pipeline.base_dir, pipeline.base_dir_was_specified)
else:
print_crash_files_and_exit(args.logname, pipeline.base_dir)caps_directory=self.absolute_path(args.caps_directory),
tsv_file=self.absolute_path(args.subjects_sessions_tsv),
base_dir=self.absolute_path(args.working_directory),
low_bval=args.low_bval,
)
if args.n_procs:
exec_pipeline = pipeline.run(plugin='MultiProc',
plugin_args={'n_procs': args.n_procs})
else:
exec_pipeline = pipeline.run()
if isinstance(exec_pipeline, Graph):
print_end_pipeline(self.name, pipeline.base_dir, pipeline.base_dir_was_specified)
else:
print_crash_files_and_exit(args.logname, pipeline.base_dir)group_id=args.group_id)
pipeline.parameters.update({
'tissues': args.tissues
})
if args.n_procs:
exec_pipeline = pipeline.run(plugin='MultiProc',
plugin_args={'n_procs': args.n_procs})
else:
exec_pipeline = pipeline.run()
if isinstance(exec_pipeline, Graph):
print_end_pipeline(self.name, pipeline.base_dir, pipeline.base_dir_was_specified)
else:
print_crash_files_and_exit(args.logname, pipeline.base_dir)pipeline.parameters['full_width_at_half_maximum'],
pipeline.tsv_file)
cprint("Parameters used for this pipeline:")
cprint(pipeline.parameters)
if args.n_procs:
exec_pipeline = pipeline.run(plugin='MultiProc',
plugin_args={'n_procs': args.n_procs})
else:
exec_pipeline = pipeline.run()
if isinstance(exec_pipeline, Graph):
print_end_pipeline(self.name, pipeline.base_dir, pipeline.base_dir_was_specified)
else:
print_crash_files_and_exit(args.logname, pipeline.base_dir)'voxel_size': tuple(args.voxel_size) if args.voxel_size is not None else None,
'modulation': args.modulate,
'fwhm': args.smooth,
'atlas_list': args.atlases
})
if args.n_procs:
exec_pipeline = pipeline.run(plugin='MultiProc',
plugin_args={'n_procs': args.n_procs})
else:
exec_pipeline = pipeline.run()
if isinstance(exec_pipeline, Graph):
print_end_pipeline(self.name, pipeline.base_dir, pipeline.base_dir_was_specified)
else:
print_crash_files_and_exit(args.logname, pipeline.base_dir))
pipeline.parameters = {
'recon_all_args': args.recon_all_args
}
if args.n_procs:
exec_pipeline = pipeline.run(plugin='MultiProc',
plugin_args={'n_procs': args.n_procs})
else:
exec_pipeline = pipeline.run()
if isinstance(exec_pipeline, Graph):
print_end_pipeline(self.name, pipeline.base_dir, pipeline.base_dir_was_specified)
else:
print_crash_files_and_exit(args.logname, pipeline.base_dir)pipeline = DwiDti(
caps_directory=self.absolute_path(args.caps_directory),
tsv_file=self.absolute_path(args.subjects_sessions_tsv),
base_dir=self.absolute_path(args.working_directory)
)
if args.n_procs:
exec_pipeline = pipeline.run(plugin='MultiProc',
plugin_args={'n_procs': args.n_procs})
else:
exec_pipeline = pipeline.run()
if isinstance(exec_pipeline, Graph):
print_end_pipeline(self.name, pipeline.base_dir, pipeline.base_dir_was_specified)
else:
print_crash_files_and_exit(args.logname, pipeline.base_dir)pipeline.parameters = {
'group_id': args.group_id,
'atlases': args.atlases,
}
if args.n_procs:
exec_pipeline = pipeline.run(plugin='MultiProc',
plugin_args={'n_procs': args.n_procs})
else:
exec_pipeline = pipeline.run()
if isinstance(exec_pipeline, Graph):
print_end_pipeline(self.name, pipeline.base_dir, pipeline.base_dir_was_specified)
else:
print_crash_files_and_exit(args.logname, pipeline.base_dir)base_dir=self.absolute_path(args.working_directory)
)
pipeline.parameters = {
'pet_type': args.pet_tracer,
}
if args.n_procs:
exec_pipeline = pipeline.run(plugin='MultiProc',
plugin_args={'n_procs': args.n_procs})
else:
exec_pipeline = pipeline.run()
if isinstance(exec_pipeline, Graph):
print_end_pipeline(self.name, pipeline.base_dir, pipeline.base_dir_was_specified)
else:
print_crash_files_and_exit(args.logname, pipeline.base_dir)'fwhm': args.full_width_half_maximum,
'image_type': args.image_type,
'pet_type': args.pet_tracer,
'no_pvc': args.no_pvc
}
if args.n_procs:
exec_pipeline = pipeline.run(plugin='MultiProc',
plugin_args={'n_procs': args.n_procs})
else:
exec_pipeline = pipeline.run()
if isinstance(exec_pipeline, Graph):
print_end_pipeline(self.name, pipeline.base_dir, pipeline.base_dir_was_specified)
else:
print_crash_files_and_exit(args.logname, pipeline.base_dir)clinica
Software platform for clinical neuroimaging studies
Package Health Score
81 / 100Popular clinica functions
- clinica.bids.converters.adni_utils.replace_sequence_chars
- clinica.engine
- clinica.engine.CmdParser
- clinica.engine.cmdparser.PIPELINE_CATEGORIES
- clinica.iotools.converters.adni_to_bids.adni_utils.replace_sequence_chars
- clinica.pipelines.engine
- clinica.pipelines.engine.Pipeline
- clinica.pipelines.machine_learning.base.MLWorkflow
- clinica.pipelines.machine_learning.voxel_based_io.load_data
- clinica.pipelines.machine_learning.voxel_based_io.revert_mask
- clinica.pipelines.machine_learning.voxel_based_io.weights_to_nifti
- clinica.pipelines.machine_learning_spatial_svm.spatial_svm_utils
- clinica.pipelines.t1_freesurfer_longitudinal.t1_freesurfer_template_utils
- clinica.utils.atlas.AtlasAbstract
- clinica.utils.exceptions.ClinicaCAPSError
- clinica.utils.exceptions.ClinicaException
- clinica.utils.inputs.clinica_file_reader
- clinica.utils.stream.cprint
- clinica.utils.ux.print_crash_files_and_exit
- clinica.utils.ux.print_end_pipeline