From d7794c8d7083d8d529314141aee279f47ae61b04 Mon Sep 17 00:00:00 2001 From: mathiasg Date: Wed, 17 Mar 2021 12:56:34 -0400 Subject: [PATCH 1/2] FIX: Default to mri_coreg if using FreeSurfer --- nibabies/workflows/bold/registration.py | 18 ++++++++---------- 1 file changed, 8 insertions(+), 10 deletions(-) diff --git a/nibabies/workflows/bold/registration.py b/nibabies/workflows/bold/registration.py index 19c8c7ea..10377809 100644 --- a/nibabies/workflows/bold/registration.py +++ b/nibabies/workflows/bold/registration.py @@ -131,16 +131,14 @@ def init_bold_reg_wf( name='outputnode' ) - # if freesurfer: - # bbr_wf = init_bbreg_wf(use_bbr=use_bbr, bold2t1w_dof=bold2t1w_dof, - # bold2t1w_init=bold2t1w_init, omp_nthreads=omp_nthreads) - # else: - # bbr_wf = init_fsl_bbr_wf(use_bbr=use_bbr, bold2t1w_dof=bold2t1w_dof, - # bold2t1w_init=bold2t1w_init, sloppy=sloppy) - # Replace with volumetric registration until better WM/GM contrasts - - bbr_wf = init_fsl_bbr_wf(use_bbr=False, bold2t1w_dof=bold2t1w_dof, - bold2t1w_init=bold2t1w_init, sloppy=sloppy) + # Default to no bbr for the moment + use_bbr = False + if freesurfer: + bbr_wf = init_bbreg_wf(use_bbr=use_bbr, bold2t1w_dof=bold2t1w_dof, + bold2t1w_init=bold2t1w_init, omp_nthreads=omp_nthreads) + else: + bbr_wf = init_fsl_bbr_wf(use_bbr=use_bbr, bold2t1w_dof=bold2t1w_dof, + bold2t1w_init=bold2t1w_init, sloppy=sloppy) workflow.connect([ (inputnode, bbr_wf, [ From 5792d59da5cbfe0538238b04ec66d41a769a7fa7 Mon Sep 17 00:00:00 2001 From: mathiasg Date: Wed, 17 Mar 2021 12:56:57 -0400 Subject: [PATCH 2/2] FIX: Forgotten indentation --- nibabies/cli/parser.py | 1 + 1 file changed, 1 insertion(+) diff --git a/nibabies/cli/parser.py b/nibabies/cli/parser.py index 930517ae..48a45c1a 100644 --- a/nibabies/cli/parser.py +++ b/nibabies/cli/parser.py @@ -626,6 +626,7 @@ def parse_args(args=None, namespace=None): # Initialize --output-spaces if not defined if config.execution.output_spaces is None: # TODO: Set a default volumetric output space + pass # Retrieve logging level build_log = config.loggers.cli