def __init__(self, pipeline_mode, fs_subjects_dir=None, fs_subject_id=None, bids_dir="", output_dir=""):
RegistrationStage.__init__(self, pipeline_mode, fs_subjects_dir, fs_subject_id, bids_dir, output_dir)
self.config = RegistrationConfigUI()
self.config.pipeline = pipeline_mode
if self.config.pipeline == "fMRI":
self.config.registration_mode = 'FSL (Linear)'
self.config.registration_mode_trait = [
'FSL (Linear)', 'BBregister (FS)']
self.inputs = self.inputs + \
["eroded_csf", "eroded_wm", "eroded_brain"]
self.outputs = self.outputs + ["eroded_wm_registered_crop", "eroded_csf_registered_crop",
"eroded_brain_registered_crop"]
def __init__(
self,
pipeline_mode,
fs_subjects_dir=None,
fs_subject_id=None,
bids_dir="",
output_dir="",
):
"""Constructor of the RegistrationStageUI class.
Parameters
-----------
pipeline_mode : string
Can be 'fMRI' or 'diffusion'
fs_subjects_dir : path
Path the the FreeSurfer subjects directory
fs_subject_id : path
FreeSurfer subject label
bids_dir : path
BIDS root directory
output_dir : path
Output directory
See also
---------
cmp.stages.registration.registration.RegistrationStage.__init_
cmp.cmpbidsappmanager.stages.registration.registration.RegistrationStageUI
"""
RegistrationStage.__init__(self, pipeline_mode, fs_subjects_dir,
fs_subject_id, bids_dir, output_dir)
self.config = RegistrationConfigUI()
self.config.pipeline = pipeline_mode
if self.config.pipeline == "fMRI":
self.config.registration_mode = "FSL (Linear)"
self.config.registration_mode_trait = [
"FSL (Linear)", "BBregister (FS)"
]
self.inputs = self.inputs + [
"eroded_csf", "eroded_wm", "eroded_brain"
]
self.outputs = self.outputs + [
"eroded_wm_registered_crop",
"eroded_csf_registered_crop",
"eroded_brain_registered_crop",
]
def __init__(self, project_info):
self.subjects_dir = project_info.freesurfer_subjects_dir
self.subject_id = project_info.freesurfer_subject_id
self.global_conf.subjects = project_info.subjects
self.global_conf.subject = project_info.subject
if len(project_info.subject_sessions) > 0:
self.global_conf.subject_session = project_info.subject_session
self.subject_directory = os.path.join(self.base_directory,
project_info.subject,
project_info.subject_session)
else:
self.global_conf.subject_session = ''
self.subject_directory = os.path.join(project_info.base_directory,
project_info.subject)
self.derivatives_directory = os.path.abspath(
project_info.output_directory)
if project_info.output_directory is not None:
self.output_directory = os.path.abspath(
project_info.output_directory)
else:
self.output_directory = os.path.join(self.base_directory,
"derivatives")
self.stages = {
'Preprocessing':
PreprocessingStage(bids_dir=project_info.base_directory,
output_dir=self.output_directory),
'Registration':
RegistrationStage(
pipeline_mode="fMRI",
fs_subjects_dir=project_info.freesurfer_subjects_dir,
fs_subject_id=os.path.basename(
project_info.freesurfer_subject_id),
bids_dir=project_info.base_directory,
output_dir=self.output_directory),
'FunctionalMRI':
FunctionalMRIStage(bids_dir=project_info.base_directory,
output_dir=self.output_directory),
'Connectome':
ConnectomeStage(bids_dir=project_info.base_directory,
output_dir=self.output_directory)
}
Pipeline.__init__(self, project_info)
self.subject = project_info.subject
self.stages['FunctionalMRI'].config.on_trait_change(
self.update_nuisance_requirements, 'global_nuisance')
self.stages['FunctionalMRI'].config.on_trait_change(
self.update_nuisance_requirements, 'csf')
self.stages['FunctionalMRI'].config.on_trait_change(
self.update_nuisance_requirements, 'wm')
self.stages['Connectome'].config.on_trait_change(
self.update_scrubbing, 'apply_scrubbing')
def __init__(self, project_info):
self.stages = {
'Segmentation': SegmentationStage(),
'Parcellation': ParcellationStage(pipeline_mode="Diffusion"),
'Preprocessing': PreprocessingStage(),
'Registration': RegistrationStage(pipeline_mode="Diffusion"),
'Diffusion': DiffusionStage(),
'MRTrixConnectome': MRTrixConnectomeStage()
}
Pipeline.__init__(self, project_info)
self.diffusion_imaging_model = project_info.diffusion_imaging_model
self.subject = project_info.subject
self.global_conf.subjects = project_info.subjects
self.global_conf.subject = self.subject
self.subject_directory = os.path.join(self.base_directory,
self.subject)
self.derivatives_directory = os.path.join(self.base_directory,
'derivatives')
self.stages['Segmentation'].config.on_trait_change(
self.update_parcellation, 'seg_tool')
self.stages['Parcellation'].config.on_trait_change(
self.update_segmentation, 'parcellation_scheme')
def __init__(self, project_info):
self.stages = {
'Preprocessing': PreprocessingStage(),
'Segmentation': SegmentationStage(),
'Parcellation': ParcellationStage(pipeline_mode="Diffusion"),
'Registration': RegistrationStage(pipeline_mode="Diffusion"),
'Diffusion': DiffusionStage(),
'Connectome': ConnectomeStage()
}
Pipeline.__init__(self, project_info)
self.stages['Segmentation'].config.on_trait_change(
self.update_parcellation, 'seg_tool')
self.stages['Parcellation'].config.on_trait_change(
self.update_segmentation, 'parcellation_scheme')
def __init__(self, project_info):
self.stages = {
'Preprocessing': PreprocessingStage(),
'Segmentation': SegmentationStage(),
'Parcellation': ParcellationStage(pipeline_mode="fMRI"),
'Registration': RegistrationStage(pipeline_mode="fMRI"),
'Functional': FunctionalStage(),
'Connectome': ConnectomeStage()
}
Pipeline.__init__(self, project_info)
self.stages['Segmentation'].config.on_trait_change(
self.update_parcellation, 'seg_tool')
self.stages['Parcellation'].config.on_trait_change(
self.update_segmentation, 'parcellation_scheme')
self.stages['Functional'].config.on_trait_change(
self.update_nuisance_requirements, 'global_nuisance')
self.stages['Functional'].config.on_trait_change(
self.update_nuisance_requirements, 'csf')
self.stages['Functional'].config.on_trait_change(
self.update_nuisance_requirements, 'wm')
self.stages['Connectome'].config.on_trait_change(
self.update_scrubbing, 'apply_scrubbing')
def __init__(self, project_info):
"""Constructor of a `fMRIPipeline` object.
Parameters
----------
project_info: cmp.project.ProjectInfo
Instance of `CMP_Project_Info` object.
See Also
--------
cmp.project.CMP_Project_Info
"""
self.subjects_dir = project_info.freesurfer_subjects_dir
self.subject_id = project_info.freesurfer_subject_id
self.global_conf.subjects = project_info.subjects
self.global_conf.subject = project_info.subject
if len(project_info.subject_sessions) > 0:
self.global_conf.subject_session = project_info.subject_session
self.subject_directory = os.path.join(
project_info.base_directory,
project_info.subject,
project_info.subject_session,
)
else:
self.global_conf.subject_session = ""
self.subject_directory = os.path.join(project_info.base_directory,
project_info.subject)
self.derivatives_directory = os.path.abspath(
project_info.output_directory)
if project_info.output_directory is not None:
self.output_directory = os.path.abspath(
project_info.output_directory)
else:
self.output_directory = os.path.join(self.base_directory,
"derivatives")
self.stages = {
"Preprocessing":
PreprocessingStage(bids_dir=project_info.base_directory,
output_dir=self.output_directory),
"Registration":
RegistrationStage(
pipeline_mode="fMRI",
fs_subjects_dir=project_info.freesurfer_subjects_dir,
fs_subject_id=os.path.basename(
project_info.freesurfer_subject_id),
bids_dir=project_info.base_directory,
output_dir=self.output_directory,
),
"FunctionalMRI":
FunctionalMRIStage(bids_dir=project_info.base_directory,
output_dir=self.output_directory),
"Connectome":
ConnectomeStage(bids_dir=project_info.base_directory,
output_dir=self.output_directory),
}
Pipeline.__init__(self, project_info)
self.subject = project_info.subject
self.stages["FunctionalMRI"].config.on_trait_change(
self.update_nuisance_requirements, "global_nuisance")
self.stages["FunctionalMRI"].config.on_trait_change(
self.update_nuisance_requirements, "csf")
self.stages["FunctionalMRI"].config.on_trait_change(
self.update_nuisance_requirements, "wm")
self.stages["Connectome"].config.on_trait_change(
self.update_scrubbing, "apply_scrubbing")