Unwarping EPIs

Apply susceptibility distortion correction (SDC)

Abbreviations

fmap

fieldmap

VSM

voxel-shift map – a 3D nifti where displacements are in pixels (not mm)

DFM

displacements field map – a nifti warp file compatible with ANTs (mm)

fmriprep.workflows.fieldmap.unwarp.sdc_unwarp(name='SDC_unwarp', settings=None)

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

It also calculates a new mask for the input dataset that takes into account the distortions. The mask is restricted to the field of view of the fieldmap since outside of it corrections could not be performed.

(Source code, png, svg, pdf)

Inputs

in_reference

the reference image

in_mask

a brain mask corresponding to in_reference

name_source

path to the original _bold file being unwarped

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_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

out_mask_report

reportled for the skullstripping