aslprep.sdcflows.workflows.gre module

Processing phase-difference (aka GRE) fieldmaps.

Workflows for processing GRE fieldmaps

Workflows for preparing the magnitude part of GRE fieldmap images and cleaning up the fieldmaps created from the phases or phasediff.

init_fmap_postproc_wf(omp_nthreads, fmap_bspline, median_kernel_size=5, name='fmap_postproc_wf')

Postprocess a B0 map estimated elsewhere.

This workflow denoises (mostly via smoothing) a B0 fieldmap.

Workflow Graph

(Source code, png, svg, pdf)

Parameters:

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

• fmap_bspline (bool) – Whether the fieldmap should be smoothed and extrapolated to off-brain regions using B-Spline basis.

• median_kernel_size (int) – Size of the kernel when smoothing is done with a median filter.

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

Inputs:

• fmap_mask (pathlike) – A brain binary mask corresponding to this fieldmap.

• fmap_ref (pathlike) – A preprocessed magnitude/reference image for the fieldmap.

• fmap (pathlike) – A B0-field nonuniformity map (aka fieldmap) estimated elsewhere.

Outputs:

out_fmap (pathlike) – Postprocessed fieldmap.

init_magnitude_wf(omp_nthreads, name='magnitude_wf')

Prepare the magnitude part of GRE fieldmaps.

Average (if not done already) the magnitude part of the GRE images, run N4 to correct for B1 field nonuniformity, and skull-strip the preprocessed magnitude.

Workflow Graph

(Source code, png, svg, pdf)

Parameters:

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

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

Inputs:

magnitude (pathlike) – Path to the corresponding magnitude path(s).

Outputs:

• fmap_ref (pathlike) – Path to the fieldmap reference calculated in this workflow.

• fmap_mask (pathlike) – Path to a binary brain mask corresponding to the reference above.