aslprep.workflows.asl.util module

Utility workflows.

init_asl_reference_wf(omp_nthreads, asl_file=None, sbref_files=None, brainmask_thresh=0.1, pre_mask=False, name='asl_reference_wf', gen_report=False)[source]

Build a workflow that generates reference ASL images for a series.

The raw reference image is the target of HMC, and a contrast-enhanced reference is the subject of distortion correction, as well as boundary-based registration to T1w and template spaces.

Workflow Graph

(Source code)

Parameters:

  • omp_nthreads (int) – Maximum number of threads an individual process may use

  • asl_file (str) – ASL series NIfTI file

  • sbref_files (list or bool) – Single band (as opposed to multi band) reference NIfTI file. If True is passed, the workflow is built to accommodate SBRefs, but the input is left undefined (i.e., it is left open for connection)

  • brainmask_thresh (float) – Lower threshold for the probabilistic brainmask to obtain the final binary mask (default: 0.5).

  • pre_mask (bool) – Indicates whether the pre_mask input will be set (and thus, step 1 should be skipped).

  • name (str) – Name of workflow (default: asl_reference_wf)

  • gen_report (bool) – Whether a mask report node should be appended in the end

Inputs:

  • asl_file (str) – ASL series NIfTI file

  • asl_mask (bool) – A tentative brain mask to initialize the workflow (requires pre_mask parameter set True).

  • dummy_scans (int or None) – Number of non-steady-state volumes specified by user at beginning of asl_file

  • sbref_file (str) – single band (as opposed to multi band) reference NIfTI file

Outputs:

  • asl_file (str) – Validated ASL series NIfTI file

  • raw_ref_image (str) – Reference image to which ASL series is motion corrected

  • skip_vols (int) – Number of non-steady-state volumes selected at beginning of asl_file

  • algo_dummy_scans (int) – Number of non-steady-state volumes agorithmically detected at beginning of asl_file

  • ref_image (str) – Contrast-enhanced reference image

  • ref_image_brain (str) – Skull-stripped reference image

  • asl_mask (str) – Skull-stripping mask of reference image

  • validation_report (str) – HTML reportlet indicating whether asl_file had a valid affine

Subworkflows

  • init_enhance_and_skullstrip_wf()

init_validate_asl_wf(asl_file=None, name='validate_asl_wf')[source]

Build a workflow to validate an ASL file.

This was split out of init_asl_reference_wf(), as that workflow only takes in a subset of the ASL run (typically the M0 scans).

Workflow Graph

(Source code)

Parameters:

  • asl_file (str) – ASL series NIfTI file

  • name (str) – Name of workflow (default: validate_asl_wf)

Inputs:

asl_file (str) – ASL series NIfTI file

Outputs:

  • asl_file (str) – Validated ASL series NIfTI file

  • validation_report (str) – HTML reportlet indicating whether asl_file had a valid affine