sdcflows.workflows.unwarp module

Apply the estimated fieldmap to perform susceptibility-derived distortion correction.

sdcflows.workflows.unwarp.init_sdc_unwarp_wf(omp_nthreads, debug, name='sdc_unwarp_wf')[source]

Apply the warping given by a displacements fieldmap.

This workflow takes in a displacements field through which the input reference can be corrected for susceptibility-derived distortion.

It also calculates a new mask for the input dataset, after the distortions have been accounted for.

../_images/sdcflows-workflows-unwarp-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_warp (os.PathLike) – The DFM that corrects for susceptibility-derived distortions estimated elsewhere.

  • in_reference (os.PathLike) – the reference image to be unwarped.

  • in_reference_mask (os.PathLike) – the reference image mask to be unwarped

Outputs

  • out_reference (str) – the in_reference after unwarping

  • out_reference_brain (str) – the in_reference after unwarping and skullstripping

  • out_warp (str) – the in_warp field is forwarded for compatibility

  • out_mask (str) – mask of the unwarped input file