pymialsrtk.workflows.recon_labelmap_stage module

Module for the high-resolution reconstruction stage of low-resolution labelmaps in the super-resolution reconstruction pipeline.

pymialsrtk.workflows.recon_labelmap_stage.create_recon_labelmap_stage(p_sub_ses, p_verbose=False, name='recon_labels_stage')[source]

Create a SR reconstruction workflow for tissue label maps.

Parameters

  • p_sub_ses (string) – String containing subject-session information for output formatting

  • p_verbose (boolean) – Whether verbosity should be enabled (default: False)

  • name (string) – Name of workflow (default: “recon_labels_stage”)

Inputs

  • input_labels (list of items which are a pathlike object or string representing a file) – Input LR label maps

  • input_masks (list of items which are a pathlike object or string representing a file) – Input mask images

  • input_transforms (list of items which are a pathlike object or string representing a file) – Input tranforms

  • input_reference (pathlike object or string representing a file) – Input HR reference image

  • label_ids (list of integer) – Label IDs to reconstruct

  • stacks_order (list of integer) – Order of stacks in the reconstruction

Outputs

output_labelmap (pathlike object or string representing a file) – HR labelmap

Example

>>> from pymialsrtk.pipelines.workflows import recon_labelmap_stage as rec_label
>>> recon_labels_stage = rec_label.create_recon_labelmap_stage(
        p_sub_ses=p_sub_ses,
        p_verbose=p_verbose
    )
>>> recon_labels_stage.inputs.input_labels = [
        'sub-01_run-1_labels.nii.gz',
        'sub-01_run-2_labels.nii.gz'
    ]
>>> recon_labels_stage.inputs.input_masks = [
        'sub-01_run-1_T2w.nii_mask.gz',
        'sub-01_run-2_T2w.nii_mask.gz'
    ]
>>> recon_labels_stage.inputs.input_transforms = [
        'sub-01_run-1_transforms.txt',
        'sub-01_run-2_transforms.txt'
    ]
>>> recon_labels_stage.inputs.input_reference = 'sub-01_desc-GT_T2w.nii.gz'
>>> recon_labels_stage.inputs.label_ids = 'sub-01_desc-GT_T2w.nii.gz'
>>> recon_labels_stage.inputs.stacks_order = [2,1]
>>> recon_labels_stage.run()