aslprep.workflows.asl.reference module

Workflows for generating reference images.

init_raw_aslref_wf(*, asl_file=None, m0scan=False, use_ge=False, name='raw_aslref_wf')[source]

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

CBF images have the best GM-WM contrast, but raw ASL files rarely have precomputed CBF volumes. As such, ASLPrep will select volumes in the following order: CBF, M0, deltam, control.

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
../_images/aslprep-workflows-asl-reference-1.png

(Source code, png, svg, pdf)

Parameters:

  • asl_file (str) – ASL series NIfTI file

  • m0scan (bool) – True if a separate M0 file is available. False if not.

  • use_ge (bool) – If True, the M0 scan (when available) will be prioritized as the volume type for the reference image, as GE deltam volumes exhibit extreme background noise.

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

Inputs:

  • asl_file (str) – ASL series NIfTI file

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

Outputs:

  • asl_file (str) – Validated BOLD series NIfTI file

  • aslref (str) – Reference image to which BOLD 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 algorithmically detected at beginning of asl_file