asldro.pipelines package

Submodules

asldro.pipelines.asl_quantification module

asldro.pipelines.check_nifti_units module

asldro.pipelines.check_nifti_units.check_nifti_units()

asldro.pipelines.combine_masks module

Pipeline to combine fuzzy masks into a single segmentation mask

asldro.pipelines.combine_masks.combine_fuzzy_masks(params_filename: str, output_filename: str = None) → asldro.containers.image.BaseImageContainer

Combines fuzzy masks into a single segmentation mask image.

Parameters

  • params_filename (str) – Path to the combining masks parameter JSON file.

  • output_filename (str) – Path to the output combined mask NIFTI image, defaults to None

Returns

The combined mask, as an image container.

Return type

BaseImageContainer

asldro.pipelines.create_qasper_ground_truth module

asldro.pipelines.generate_ground_truth module

Pipeline to generate a ground truth image and save

asldro.pipelines.generate_ground_truth.generate_hrgt(hrgt_params_filename: str, seg_mask_filename: str, output_dir: str = None) → dict

Generates a high-resolution ground truth (hrgt) based on:

  • A segmentation mask image

  • A file describing what values to assign to each region.

The hrgt is saved in the folder output_dir

Parameters

  • hrgt_params_filename (str) – Path to the hrgt parameter JSON file

  • seg_mask_filename (str) – Path to the segmentation mask NIFTI image

  • output_dir (str, optional) – Directory to save files to, defaults to None

Returns

dictionary containing the ground truth image, and the ground truth parameter file

Return type

dict

Module contents