sdcflows.workflows.fmap module

Fieldmap-based estimation of susceptibility distortions.

Direct B0 mapping sequences

When the fieldmap is directly measured with a prescribed sequence (such as SE), we only need to calculate the corresponding displacements field that accounts for the distortions. This procedure is described with more detail here.

This corresponds to this section of the BIDS specification.

sdcflows.workflows.fmap.init_fmap2field_wf(omp_nthreads, debug, name='fmap2field_wf', generate_report=True)[source]

Convert the estimated fieldmap in Hz into a displacements field.

This workflow takes in a fieldmap and calculates the corresponding displacements field (in other words, an ANTs-compatible warp file).

Workflow Graph
../_images/sdcflows-workflows-fmap-1.png

(Source code, png, svg, pdf)

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

  • debug (bool) – Run fast configurations of registrations.

  • name (str) – Unique name of this workflow.

Inputs
  • in_reference – the reference image

  • in_reference_brain – the reference image (skull-stripped)

  • metadata – metadata associated to the in_reference EPI input

  • fmap – the fieldmap in Hz

  • fmap_ref – the reference (anatomical) image corresponding to fmap

  • fmap_mask – a brain mask corresponding to fmap

Outputs
  • out_reference – the in_reference after unwarping

  • out_reference_brain – the in_reference after unwarping and skullstripping

  • out_warp – the corresponding DFM compatible with ANTs

  • out_jacobian – the jacobian of the field (for drop-out alleviation)

  • out_mask – mask of the unwarped input file

sdcflows.workflows.fmap.init_fmap_wf(omp_nthreads, fmap_bspline, name='fmap_wf')[source]

Estimate the fieldmap based on a field-mapping MRI acquisition.

When we have a sequence that directly measures the fieldmap, we just need to mask it (using the corresponding magnitude image) to remove the noise in the surrounding air region, and ensure that units are Hz.

Workflow Graph
../_images/sdcflows-workflows-fmap-2.png

(Source code, png, svg, pdf)

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

  • fmap_bspline (bool) – Whether the fieldmap estimate will be smoothed using BSpline basis.

  • name (str) – Unique name of this workflow.

Inputs
  • magnitude (str) – Path to the corresponding magnitude image for anatomical reference.

  • fieldmap (str) – Path to the fieldmap acquisition (*_fieldmap.nii[.gz] of BIDS).

Outputs
  • fmap (str) – Path to the estimated fieldmap.

  • fmap_ref (str) – Path to a preprocessed magnitude image reference.

  • fmap_mask (str) – Path to a binary brain mask corresponding to the fmap and fmap_ref pair.