diff --git a/qsiprep/cli/run.py b/qsiprep/cli/run.py index 902f6675..ad4a989e 100644 --- a/qsiprep/cli/run.py +++ b/qsiprep/cli/run.py @@ -447,7 +447,7 @@ def get_parser(): action='store', default='TOPUP', choices=['TOPUP', 'DRBUDDI'], - help='select which SDC method to use for PEPOLAR fieldmaps (default: OASIS)') + help='select which SDC method to use for PEPOLAR fieldmaps (default: TOPUP)') g_fmap.add_argument( '--denoised_image_sdc', '--denoised_image_sdc', @@ -480,6 +480,12 @@ def get_parser(): default=False, help='EXPERIMENTAL: Use fieldmap-free distortion correction. To use ' 'this option, "template" must be passed to --output-space') + g_syn.add_argument( + '--syn-method', '-syn_method', + action='store_true', + default='synb0', + help='Mehtod for SYN unwarping. Options are ' + 'synb0 (default) and ANTs') g_syn.add_argument( '--force-syn', '--force_syn', action='store_true', @@ -995,6 +1001,7 @@ def build_qsiprep_workflow(opts, retval): fmap_bspline=opts.fmap_bspline, fmap_demean=opts.fmap_no_demean, use_syn=opts.use_syn_sdc, + syn_method=opts.syn_method, force_syn=opts.force_syn ) retval['return_code'] = 0