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'])
