qsiprep.workflows.fieldmap.pepolar module

Phase Encoding POLARity (PEPOLAR) distortion correction workflows.

Phase Encoding POLARity (PEPOLAR) techniques

qsiprep.workflows.fieldmap.pepolar.init_extended_pepolar_report_wf(segment_t2w, omp_nthreads=1, name='extended_pepolar_report_wf')

qsiprep.workflows.fieldmap.pepolar.init_prepare_dwi_epi_wf(omp_nthreads, orientation='LPS', name='prepare_epi_wf')

Build a workflow that prepares a 3D b=0 reference for distortion estimation.

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.