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)[source]¶ 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