pyalfe.tasks.registration

pyalfe.tasks.registration#

class pyalfe.tasks.registration.CrossModalityRegistration(image_registration: ImageRegistration, pipeline_dir: PipelineDataDir, modalities_all: list[Modality], modalities_target: list[Modality], image_type: str = 'skullstripped', overwrite: bool = True)[source]#

Bases: object

This task registers all the modalities to target modalities.

image_registration#

The image registration object.

Type:

ImageRegistration

pipeline_dir#

The pipeline data directory object.

Type:

PipelineDataDir

modalities_all#

All the modalities that should be registered to the target modalities.

Type:

list[Modality]

modalities_target#

Target modalities.

Type:

list[Modality]

image_type#

The type of image that should be registered. Default is skullstripped.

Type:

str

overwrite#

Whether to overwrite existing registered images. Default is True.

Type:

bool

logger = <Logger CrossModalityRegistration (DEBUG)>#
run(accession)[source]#
class pyalfe.tasks.registration.Resampling(image_processor: ImageProcessor, image_registration: ImageRegistration, pipeline_dir: PipelineDataDir, modalities_target, image_type: str = 'skullstripped', overwrite=True)[source]#

Bases: object

This task resamples all the ROIs in the T1 space to the target modalities.

image_processor#

The image processor object.

Type:

ImageProcessor

image_registration#

Image registration object.

Type:

ImageRegistration

pipeline_dir#

The pipeline data directory object.

Type:

PipelineDataDir

modalities_target#

Target modalities.

Type:

list[Modality]

image_type#

The type of image that should be registered. Default is skullstripped.

Type:

str

overwrite#

Whether to overwrite existing registered images. Default is True.

Type:

bool

logger = <Logger Resampling (DEBUG)>#
run(accession)[source]#
class pyalfe.tasks.registration.T1Registration(image_processor: ImageProcessor, image_registration: ImageRegistration, pipeline_dir: PipelineDataDir, overwrite: bool = True)[source]#

Bases: object

This task registers anatomical templates to the T1 image.

image_processor#

Image processor object.

Type:

ImageProcessor

image_registration#

Image registration object.

Type:

ImageRegistration

pipeline_dir#

The pipeline data directory object.

Type:

PipelineDataDir

overwrite#

Whether to overwrite existing registered images. Default is True.

Type:

bool

logger = <Logger T1Registration (DEBUG)>#
run(accession)[source]#