asl_pipeline

asl_pipeline ¶

ASL analysis pipeline.

This module provides an end-to-end ASL analysis pipeline, integrating M0 calibration and CBF quantification following the OSIPI ASL Lexicon conventions.

References

.. [1] OSIPI ASL Lexicon, https://osipi.github.io/ASL-Lexicon/ .. [2] Suzuki Y et al. MRM 2024;91(4):1411-1421.

ASLPipelineConfig `dataclass` ¶

ASLPipelineConfig(
    labeling_scheme=PCASL,
    pld=1800.0,
    label_duration=1800.0,
    t1_blood=1650.0,
    labeling_efficiency=0.85,
    m0_method="single",
    output_dir=None,
)

Configuration for ASL pipeline.

ATTRIBUTE	DESCRIPTION
`labeling_scheme`	ASL labeling scheme. TYPE: `LabelingScheme`
`pld`	Post-labeling delay in milliseconds. TYPE: `float`
`label_duration`	Labeling duration in milliseconds (for pCASL/CASL). TYPE: `float`
`t1_blood`	Blood T1 in milliseconds. TYPE: `float`
`labeling_efficiency`	Labeling efficiency. TYPE: `float`
`m0_method`	M0 calibration method: 'single', 'voxelwise', or 'reference_region'. TYPE: `str`
`output_dir`	Output directory for results. TYPE: `Path \| None`

ASLPipelineResult `dataclass` ¶

ASLPipelineResult(cbf_result, m0_map, config)

Result of ASL pipeline.

ATTRIBUTE	DESCRIPTION
`cbf_result`	CBF quantification results. TYPE: `ASLQuantificationResult`
`m0_map`	M0 values used. TYPE: `NDArray \| None`
`config`	Pipeline configuration used. TYPE: `ASLPipelineConfig`

ASLPipeline ¶

ASLPipeline(config=None)

End-to-end ASL analysis pipeline.

This pipeline performs: 1. ASL difference computation (label - control) 2. M0 calibration 3. CBF quantification

Examples:

>>> from osipy.pipeline import ASLPipeline, ASLPipelineConfig
>>> from osipy.asl import LabelingScheme
>>> config = ASLPipelineConfig(
...     labeling_scheme=LabelingScheme.PCASL,
...     pld=1800.0,
... )
>>> pipeline = ASLPipeline(config)
>>> result = pipeline.run(label_images, control_images, m0_image)

Initialize ASL pipeline.

PARAMETER	DESCRIPTION
`config`	Pipeline configuration. TYPE: `ASLPipelineConfig \| None` DEFAULT: `None`

run ¶

run(
    label_data,
    control_data,
    m0_data,
    mask=None,
    progress_callback=None,
)

Run ASL analysis pipeline.

PARAMETER	DESCRIPTION
`label_data`	Label images, shape (...) or (..., n_averages). TYPE: `NDArray`
`control_data`	Control images, shape (...) or (..., n_averages). TYPE: `NDArray`
`m0_data`	M0 calibration image or single value. TYPE: `NDArray or float`
`mask`	Brain mask. TYPE: `NDArray` DEFAULT: `None`
`progress_callback`	Callback for progress updates. TYPE: `Callable` DEFAULT: `None`

RETURNS	DESCRIPTION
`ASLPipelineResult`	Pipeline results.

run_from_alternating ¶

run_from_alternating(
    asl_data,
    m0_data,
    label_control_order="label_first",
    mask=None,
    progress_callback=None,
)

Run ASL pipeline from interleaved label/control data.

PARAMETER	DESCRIPTION
`asl_data`	Interleaved ASL data, shape (..., n_pairs2). TYPE:* `NDArray`
`m0_data`	M0 calibration data. TYPE: `NDArray or float`
`label_control_order`	Order: 'label_first' or 'control_first'. TYPE: `str` DEFAULT: `'label_first'`
`mask`	Brain mask. TYPE: `NDArray` DEFAULT: `None`
`progress_callback`	Progress callback. TYPE: `Callable` DEFAULT: `None`

RETURNS	DESCRIPTION
`ASLPipelineResult`	Pipeline results.