aslprep.workflows.asl.reference module

Workflows for generating reference images.

init_enhance_and_skullstrip_asl_wf(disable_n4=False, name='enhance_and_skullstrip_asl_wf', omp_nthreads=1, pre_mask=False)[source]

Enhance and run brain extraction on an ASL image.

This is a modified version of the enhance_and_skullstrip_bold_wf workflow from niworkflows, with an added disable_n4 parameter to disable N4 bias field correction, which tends to be unstable on data with prescan normalization enabled.

Parameters:

  • disable_n4 (bool) – If True, N4 bias field correction will be disabled.

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

  • omp_nthreads (int) – number of threads available to parallel nodes

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

Inputs:

  • in_file (str) – BOLD image (single volume)

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

Outputs:

  • bias_corrected_file (str) – the in_file after N4 bias field correction. If disable_n4 is True, this will be the same as in_file.

  • skull_stripped_file (str) – the bias_corrected_file after skull-stripping

  • mask_file (str) – mask of the skull-stripped input file

  • out_report (str) – reportlet for the skull-stripping

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

Build a workflow that generates reference ASL 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

  • reference_volume_type (str) – Type of reference volume to use.

  • 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

Outputs:

  • asl_file (str) – Validated ASL series NIfTI file

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

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