def check_pipeline_parameters(self): """Check pipeline parameters.""" from clinica.utils.group import check_group_label from clinica.utils.atlas import T1_VOLUME_ATLASES self.parameters.setdefault("group_label", None) check_group_label(self.parameters["group_label"]) self.parameters.setdefault("atlases", T1_VOLUME_ATLASES)
def check_pipeline_parameters(self): """Check pipeline parameters.""" from clinica.utils.group import check_group_label if 'group_label' not in self.parameters.keys(): raise KeyError('Missing compulsory group_label key in pipeline parameter.') if 'tissues' not in self.parameters.keys(): self.parameters['tissues'] = [1, 2, 3] check_group_label(self.parameters['group_label'])
def check_pipeline_parameters(self): """Check pipeline parameters.""" from clinica.utils.group import check_group_label if "group_label" not in self.parameters.keys(): raise KeyError( "Missing compulsory group_label key in pipeline parameter.") self.parameters.setdefault("tissues", [1, 2, 3]) check_group_label(self.parameters["group_label"])
def check_pipeline_parameters(self): """Check pipeline parameters.""" from clinica.utils.group import check_group_label if "group_label" not in self.parameters.keys(): raise KeyError( "Missing compulsory group_label key in pipeline parameter.") if "dartel_tissues" not in self.parameters.keys(): self.parameters["dartel_tissues"] = [1, 2, 3] check_group_label(self.parameters["group_label"])
def check_pipeline_parameters(self): """Check pipeline parameters.""" from .statistics_surface_utils import get_t1_freesurfer_custom_file from clinica.utils.exceptions import ClinicaException from clinica.utils.group import check_group_label if 'custom_file' not in self.parameters.keys(): self.parameters['custom_file'] = get_t1_freesurfer_custom_file() if 'feature_label' not in self.parameters.keys(): self.parameters['feature_label'] = 'ct', if 'full_width_at_half_maximum' not in self.parameters.keys(): self.parameters['full_width_at_half_maximum'] = 20 if 'threshold_uncorrected_pvalue' not in self.parameters.keys(): self.parameters['threshold_uncorrected_pvalue'] = 0.001 if 'threshold_corrected_pvalue' not in self.parameters.keys(): self.parameters['threshold_corrected_pvalue'] = 0.05, if 'cluster_threshold' not in self.parameters.keys(): self.parameters['cluster_threshold'] = 0.001, check_group_label(self.parameters['group_label']) if self.parameters['glm_type'] not in [ 'group_comparison', 'correlation' ]: raise ClinicaException( "The glm_type you specified is wrong: it should be group_comparison or " "correlation (given value: %s)." % self.parameters['glm_type']) if self.parameters['full_width_at_half_maximum'] not in [ 0, 5, 10, 15, 20 ]: raise ClinicaException( "FWHM for the surface smoothing you specified is wrong: it should be 0, 5, 10, 15 or 20 " "(given value: %s)." % self.parameters['full_width_at_half_maximum']) if self.parameters[ 'threshold_uncorrected_pvalue'] < 0 or self.parameters[ 'threshold_uncorrected_pvalue'] > 1: raise ClinicaException( "Uncorrected p-value threshold should be a lower than 1 " "(given value: %s)." % self.parameters['threshold_uncorrected_pvalue']) if self.parameters['threshold_corrected_pvalue'] < 0 or self.parameters[ 'threshold_corrected_pvalue'] > 1: raise ClinicaException( "Corrected p-value threshold should be between 0 and 1 " "(given value: %s)." % self.parameters['threshold_corrected_pvalue']) if self.parameters['cluster_threshold'] < 0 or self.parameters[ 'cluster_threshold'] > 1: raise ClinicaException( "Cluster threshold should be between 0 and 1 " "(given value: %s)." % self.parameters['cluster_threshold'])
def check_pipeline_parameters(self): """Check pipeline parameters.""" from clinica.utils.group import check_group_label default_atlases = [ 'AAL2', 'LPBA40', 'Neuromorphometrics', 'AICHA', 'Hammers' ] if 'group_id' not in self.parameters.keys(): raise KeyError( 'Missing compulsory group_id key in pipeline parameter.') if 'atlases' not in self.parameters.keys(): self.parameters['atlases'] = default_atlases check_group_label(self.parameters['group_id'])
def check_pipeline_parameters(self): """Check pipeline parameters.""" from clinica.utils.exceptions import ClinicaException from clinica.utils.group import check_group_label from .statistics_surface_utils import get_t1_freesurfer_custom_file # Clinica compulsory parameters self.parameters.setdefault("group_label", None) check_group_label(self.parameters["group_label"]) if "orig_input_data" not in self.parameters.keys(): raise KeyError( "Missing compulsory orig_input_data key in pipeline parameter." ) self.parameters.setdefault("glm_type", None) if self.parameters["glm_type"] not in ["group_comparison", "correlation"]: raise ClinicaException( f"The glm_type you specified is wrong: it should be group_comparison or " f"correlation (given value: {self.parameters['glm_type']})." ) if "contrast" not in self.parameters.keys(): raise KeyError("Missing compulsory contrast key in pipeline parameter.") # Optional parameters self.parameters.setdefault("covariates", None) self.parameters.setdefault("full_width_at_half_maximum", 20) # Optional parameters for inputs from pet-surface pipeline self.parameters.setdefault("acq_label", None) self.parameters.setdefault("suvr_reference_region", None) # Optional parameters for custom pipeline self.parameters.setdefault("custom_file", get_t1_freesurfer_custom_file()) self.parameters.setdefault("measure_label", "ct") # Advanced parameters self.parameters.setdefault("cluster_threshold", 0.001) if ( self.parameters["cluster_threshold"] < 0 or self.parameters["cluster_threshold"] > 1 ): raise ClinicaException( f"Cluster threshold should be between 0 and 1 " f"(given value: {self.parameters['cluster_threshold']})." )
def check_pipeline_parameters(self): """Check pipeline parameters.""" from clinica.utils.atlas import PET_VOLUME_ATLASES from clinica.utils.group import check_group_label self.parameters.setdefault("group_label", None) check_group_label(self.parameters["group_label"]) if "acq_label" not in self.parameters.keys(): raise KeyError("Missing compulsory acq_label key in pipeline parameter.") self.parameters.setdefault("pvc_psf_tsv", None) self.parameters.setdefault("mask_tissues", [1, 2, 3]) self.parameters.setdefault("mask_threshold", 0.3) self.parameters.setdefault("pvc_mask_tissues", [1, 2, 3]) self.parameters.setdefault("smooth", [8]) self.parameters.setdefault("atlases", PET_VOLUME_ATLASES)
def check_pipeline_parameters(self): """Check pipeline parameters.""" from clinica.utils.group import check_group_label if 'group_id' not in self.parameters.keys(): raise KeyError('Missing compulsory group_id key in pipeline parameter.') if 'fwhm' not in self.parameters.keys(): self.parameters['fwhm'] = 4 if 'image_type' not in self.parameters.keys(): self.parameters['image_type'] = 't1' if 'pet_tracer' not in self.parameters.keys(): self.parameters['pet_tracer'] = 'fdg' if 'no_pvc' not in self.parameters.keys(): self.parameters['no_pvc'] = False check_group_label(self.parameters['group_id'])
def check_pipeline_parameters(self): """Check pipeline parameters.""" from clinica.utils.group import check_group_label if 'group_label' not in self.parameters.keys(): raise KeyError('Missing compulsory group_label key in pipeline parameter.') if 'tissues' not in self.parameters: self.parameters['tissues'] = [1, 2, 3] if 'voxel_size' not in self.parameters: self.parameters['voxel_size'] = None if 'modulate' not in self.parameters: self.parameters['modulate'] = True if 'smooth' not in self.parameters: self.parameters['smooth'] = [8] check_group_label(self.parameters['group_label'])
def check_pipeline_parameters(self): """Check pipeline parameters.""" from clinica.utils.group import check_group_label if "group_label" not in self.parameters.keys(): raise KeyError( "Missing compulsory group_label key in pipeline parameter.") if "tissues" not in self.parameters: self.parameters["tissues"] = [1, 2, 3] if "voxel_size" not in self.parameters: self.parameters["voxel_size"] = None if "modulate" not in self.parameters: self.parameters["modulate"] = True if "smooth" not in self.parameters: self.parameters["smooth"] = [8] check_group_label(self.parameters["group_label"])
def check_pipeline_parameters(self): """Check pipeline parameters.""" from .statistics_surface_utils import get_t1_freesurfer_custom_file from clinica.utils.exceptions import ClinicaException from clinica.utils.group import check_group_label # Clinica compulsory parameters self.parameters.setdefault('group_label', None) check_group_label(self.parameters['group_label']) if 'orig_input_data' not in self.parameters.keys(): raise KeyError('Missing compulsory orig_input_data key in pipeline parameter.') self.parameters.setdefault('glm_type', None) if self.parameters['glm_type'] not in ['group_comparison', 'correlation']: raise ClinicaException( f"The glm_type you specified is wrong: it should be group_comparison or " f"correlation (given value: {self.parameters['glm_type']})." ) if 'contrast' not in self.parameters.keys(): raise KeyError('Missing compulsory contrast key in pipeline parameter.') # Optional parameters self.parameters.setdefault('covariates', None) self.parameters.setdefault('full_width_at_half_maximum', 20) # Optional parameters for inputs from pet-surface pipeline self.parameters.setdefault('acq_label', None) self.parameters.setdefault('suvr_reference_region', None) # Optional parameters for custom pipeline self.parameters.setdefault('custom_file', get_t1_freesurfer_custom_file()) self.parameters.setdefault('measure_label', 'ct') # Advanced parameters self.parameters.setdefault('cluster_threshold', 0.001) if self.parameters['cluster_threshold'] < 0 or self.parameters['cluster_threshold'] > 1: raise ClinicaException( f"Cluster threshold should be between 0 and 1 " f"(given value: {self.parameters['cluster_threshold']})." )
def check_pipeline_parameters(self): """Check pipeline parameters.""" from clinica.utils.group import check_group_label # Clinica compulsory parameters self.parameters.setdefault('group_label', None) check_group_label(self.parameters['group_label']) if 'orig_input_data' not in self.parameters.keys(): raise KeyError( 'Missing compulsory orig_input_data key in pipeline parameter.' ) # Optional parameters for inputs from pet-volume pipeline self.parameters.setdefault('acq_label', None) self.parameters.setdefault('suvr_reference_region', None) self.parameters.setdefault('use_pvc_data', False) # Advanced parameters self.parameters.setdefault('fwhm', 4)
def check_pipeline_parameters(self): """Check pipeline parameters.""" from clinica.utils.group import check_group_label # Clinica compulsory parameters self.parameters.setdefault("group_label", None) check_group_label(self.parameters["group_label"]) if "orig_input_data" not in self.parameters.keys(): raise KeyError( "Missing compulsory orig_input_data key in pipeline parameter." ) # Optional parameters for inputs from pet-volume pipeline self.parameters.setdefault("acq_label", None) self.parameters.setdefault("suvr_reference_region", None) self.parameters.setdefault("use_pvc_data", False) # Advanced parameters self.parameters.setdefault("fwhm", 4)
def check_pipeline_parameters(self): """Check pipeline parameters.""" from clinica.utils.exceptions import ClinicaException from clinica.utils.group import check_group_label # Clinica compulsory parameters self.parameters.setdefault("group_label", None) check_group_label(self.parameters["group_label"]) if "orig_input_data_volume" not in self.parameters.keys(): raise KeyError( "Missing compulsory orig_input_data_volume key in pipeline parameter." ) if "contrast" not in self.parameters.keys(): raise KeyError( "Missing compulsory contrast key in pipeline parameter.") # Optional parameters self.parameters.setdefault("group_label_dartel", "*") self.parameters.setdefault("full_width_at_half_maximum", 8) # Optional parameters for inputs from pet-volume pipeline self.parameters.setdefault("acq_label", None) self.parameters.setdefault("suvr_reference_region", None) self.parameters.setdefault("use_pvc_data", False) # Optional parameters for custom pipeline self.parameters.setdefault("measure_label", None) self.parameters.setdefault("custom_file", None) # Advanced parameters self.parameters.setdefault("cluster_threshold", 0.001) if (self.parameters["cluster_threshold"] < 0 or self.parameters["cluster_threshold"] > 1): raise ClinicaException( "Cluster threshold should be between 0 and 1 " "(given value: %s)." % self.parameters["cluster_threshold"])
def check_pipeline_parameters(self): """Check pipeline parameters.""" from clinica.utils.exceptions import ClinicaException from clinica.utils.group import check_group_label # Clinica compulsory parameters self.parameters.setdefault('group_label', None) check_group_label(self.parameters['group_label']) if 'orig_input_data' not in self.parameters.keys(): raise KeyError( 'Missing compulsory orig_input_data key in pipeline parameter.' ) if 'contrast' not in self.parameters.keys(): raise KeyError( 'Missing compulsory contrast key in pipeline parameter.') # Optional parameters self.parameters.setdefault('group_label_dartel', '*') self.parameters.setdefault('full_width_at_half_maximum', 8) # Optional parameters for inputs from pet-volume pipeline self.parameters.setdefault('acq_label', None) self.parameters.setdefault('suvr_reference_region', None) self.parameters.setdefault('use_pvc_data', False) # Optional parameters for custom pipeline self.parameters.setdefault('measure_label', None) self.parameters.setdefault('custom_file', None) # Advanced parameters self.parameters.setdefault('cluster_threshold', 0.001) if self.parameters['cluster_threshold'] < 0 or self.parameters[ 'cluster_threshold'] > 1: raise ClinicaException( "Cluster threshold should be between 0 and 1 " "(given value: %s)." % self.parameters['cluster_threshold'])
def check_pipeline_parameters(self): """Check pipeline parameters.""" from clinica.utils.group import check_group_label default_atlases = ['AAL2', 'LPBA40', 'Neuromorphometrics', 'AICHA', 'Hammers'] if 'group_id' not in self.parameters.keys(): raise KeyError('Missing compulsory group_id key in pipeline parameter.') if 'psf_tsv' not in self.parameters.keys(): self.parameters['psf_tsv'] = None if 'pet_tracer' not in self.parameters.keys(): self.parameters['pet_tracer'] = 'fdg' if 'mask_tissues' not in self.parameters.keys(): self.parameters['mask_tissues'] = [1, 2, 3] if 'mask_threshold' not in self.parameters.keys(): self.parameters['mask_threshold'] = 0.3 if 'pvc_mask_tissues' not in self.parameters.keys(): self.parameters['pvc_mask_tissues'] = [1, 2, 3] if 'smooth' not in self.parameters.keys(): self.parameters['smooth'] = [8] if 'atlases' not in self.parameters.keys(): self.parameters['atlases'] = default_atlases check_group_label(self.parameters['group_id'])