From 9c3e83390397080358e3722e7889a91537ad5b34 Mon Sep 17 00:00:00 2001 From: "Christopher J. Markiewicz" Date: Fri, 19 Sep 2025 09:10:30 -0400 Subject: [PATCH 1/2] chore: Pin nipreps/niworkflows#971 --- pyproject.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index 5f655cf05a..181797f8ba 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -27,7 +27,7 @@ dependencies = [ "nipype >= 1.9.0", "migas >= 0.4.0", "nireports >= 25.0.1", - "niworkflows >= 1.11.0", + "niworkflows @ git+https://github.com/nipreps/niworkflows.git@refs/pull/971/head", "nitransforms >= 25.0.1", "numpy >= 2.0", "pybids >= 0.16.4", From 1d90e1d7d7c83e10468aa3463fe10b6949940752 Mon Sep 17 00:00:00 2001 From: "Christopher J. Markiewicz" Date: Fri, 19 Sep 2025 09:14:06 -0400 Subject: [PATCH 2/2] feat: Add N4 parameters to init_syn_preprocessing_wf --- sdcflows/workflows/fit/syn.py | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/sdcflows/workflows/fit/syn.py b/sdcflows/workflows/fit/syn.py index 57ef8251eb..b303c482d6 100644 --- a/sdcflows/workflows/fit/syn.py +++ b/sdcflows/workflows/fit/syn.py @@ -348,6 +348,10 @@ def init_syn_preprocessing_wf( auto_bold_nss=False, t1w_inversion=False, sd_prior=True, + n4_iterations=(50,) * 5, + n4_shrink_factor=4, + calculate_n4_spline_grid=False, + **kwargs, ): """ Prepare EPI references and co-registration to anatomical for SyN. @@ -470,6 +474,9 @@ def init_syn_preprocessing_wf( epi_reference_wf = init_epi_reference_wf( omp_nthreads=omp_nthreads, auto_bold_nss=auto_bold_nss, + n4_iterations=n4_iterations, + n4_shrink_factor=n4_shrink_factor, + calculate_bspline_grid=calculate_n4_spline_grid, ) epi_brain = pe.Node(BrainExtraction(), name='epi_brain') merge_output = pe.Node(