sdcflows.workflows.apply.registration module

Align the fieldmap reference map to the target EPI.

The fieldmap reference map may be a magnitude image (or an EPI dataset, in the case of PEPOLAR estimation).

The target EPI is the distorted dataset (or a reference thereof).

sdcflows.workflows.apply.registration.init_coeff2epi_wf(omp_nthreads, sloppy=False, debug=False, write_coeff=False, name='coeff2epi_wf')[source]

Move the field coefficients on to the target (distorted) EPI space.

Workflow Graph
../_images/sdcflows-workflows-apply-registration-1.png

(Source code, png, svg, pdf)

Parameters:

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

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

  • debug (bool) – Run in debug mode, that is, generating additional traces of performance.

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

  • write_coeff (bool) – Map coefficients file

Inputs:

  • target_ref – the target EPI reference image

  • target_mask – the reference image (skull-stripped)

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

  • fmap_mask – a brain mask corresponding to fmap

  • fmap_coeff – fieldmap coefficients

Outputs:

  • fmap_coeff – fieldmap coefficients in the space of the target reference EPI

  • target_ref – the target reference EPI resampled into the fieldmap reference for quality control purposes.

  • target2fmap_xfm – An ITK-style transform produced with ANTs that can be used as transform in antsApplyTransforms with the fieldmap as reference and the target EPI as moving, resampling the latter into the fieldmap space.