qsiprep.workflows.fieldmap.pepolar module
Phase Encoding POLARity (PEPOLAR) techniques
- qsiprep.workflows.fieldmap.pepolar.init_extended_pepolar_report_wf(segment_t2w, omp_nthreads=1, name='extended_pepolar_report_wf')[source]
- qsiprep.workflows.fieldmap.pepolar.init_pepolar_unwarp_wf(dwi_meta, epi_fmaps, name='pepolar_unwarp_wf')[source]
This workflow takes in a set of EPI files with opposite phase encoding direction than the target file and calculates a displacements field (in other words, an ANTs-compatible warp file).
This procedure works if there is only one ‘_epi’ file is present (as long as it has the opposite phase encoding direction to the target file). The target file will be used to estimate the field distortion. However, if there is another ‘_epi’ file present with a matching phase encoding direction to the target it will be used instead.
Currently, different phase encoding dimension in the target file and the ‘_epi’ file(s) (for example ‘i’ and ‘j’) is not supported.
The warp field correcting for the distortions is estimated using AFNI’s 3dQwarp, with displacement estimation limited to the target file phase encoding direction.
It also calculates a new mask for the input dataset that takes into account the distortions.
Inputs
- in_reference
the reference image
- in_reference_brain
the reference image skullstripped
- in_mask
a brain mask corresponding to
in_reference
Outputs
- out_reference
the
in_referenceafter unwarping- out_warp
the corresponding DFM compatible with ANTs
- qsiprep.workflows.fieldmap.pepolar.init_prepare_dwi_epi_wf(omp_nthreads, orientation='LPS', name='prepare_epi_wf')[source]
This workflow takes in a set of dwi files with with the same phase encoding direction and returns a single 3D volume ready to be used in field distortion estimation. It removes b>0 volumes.
The procedure involves: estimating a robust template using FreeSurfer’s ‘mri_robust_template’, bias field correction using ANTs N4BiasFieldCorrection and AFNI 3dUnifize, skullstripping using FSL BET and AFNI 3dAutomask, and rigid coregistration to the reference using ANTs.