qsiprep.workflows.fieldmap.unwarp module

Workflows for unwarping susceptibility distortions with a fieldmap.

Unwarping

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)

qsiprep.workflows.fieldmap.unwarp.init_fmap_unwarp_report_wf(name='fmap_unwarp_report_wf')

Build a workflow that generates a reportlet showing the effect of fieldmap unwarping.

This workflow generates and saves a reportlet showing the effect of fieldmap unwarping a DWI image.

(Source code, png, svg, pdf)

Parameters:

name (str, optional) – Workflow name (default: fmap_unwarp_report_wf)

Inputs:

• in_pre – Reference image, before unwarping

• in_post – Reference image, after unwarping

• in_seg – Segmentation of preprocessed structural image, including gray-matter (GM), white-matter (WM) and cerebrospinal fluid (CSF)

• in_xfm – Affine transform from T1 space to b0 space (ITK format)

qsiprep.workflows.fieldmap.unwarp.init_sdc_unwarp_wf(name='sdc_unwarp_wf')

Build a workflow that converts a fieldmap into an ANTs-compatible warp.

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.

Inputs:

• in_reference – the reference image

• in_reference_brain – the reference image (skull-stripped)

• in_mask – a brain mask corresponding to in_reference

• 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_mask – mask of the unwarped input file

• out_hz – the fieldmap in Hz on the in_reference grid (eddy’s --field)