From 5f8516fa532dbc3f12e2042c79580e4f05917bba Mon Sep 17 00:00:00 2001 From: Chris Markiewicz Date: Thu, 18 Jul 2024 13:56:28 -0400 Subject: [PATCH 1/2] RF: Use genericised "anat" input/output for TemplateDimensions --- pyproject.toml | 2 +- smriprep/workflows/anatomical.py | 8 ++++---- 2 files changed, 5 insertions(+), 5 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index e316d11127..7bf5ae11aa 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -25,7 +25,7 @@ dependencies = [ "matplotlib >= 2.2.0", "nibabel >= 4.0.1", "nipype >= 1.7.0", - "niworkflows >= 1.10.1", + "niworkflows @ git+https://github.com/nipreps/niworkflows.git@refs/pull/879/merge", "numpy", "packaging", "pybids >= 0.11.1", diff --git a/smriprep/workflows/anatomical.py b/smriprep/workflows/anatomical.py index 78e19ad8bd..005cf047eb 100644 --- a/smriprep/workflows/anatomical.py +++ b/smriprep/workflows/anatomical.py @@ -1445,8 +1445,8 @@ def init_anat_template_wf( # fmt:off workflow.connect([ - (inputnode, anat_ref_dimensions, [('anat_files', 't1w_list')]), - (anat_ref_dimensions, denoise, [('t1w_valid_list', 'input_image')]), + (inputnode, anat_ref_dimensions, [('anat_files', 'anat_list')]), + (anat_ref_dimensions, denoise, [('anat_valid_list', 'input_image')]), (anat_ref_dimensions, anat_conform, [ ('target_zooms', 'target_zooms'), ('target_shape', 'target_shape'), @@ -1454,7 +1454,7 @@ def init_anat_template_wf( (denoise, anat_conform, [('output_image', 'in_file')]), (anat_ref_dimensions, outputnode, [ ('out_report', 'out_report'), - ('t1w_valid_list', 'anat_valid_list'), + ('anat_valid_list', 'anat_valid_list'), ]), ]) # fmt:on @@ -1524,7 +1524,7 @@ def _set_threads(in_list, maximum): # fmt:off workflow.connect([ - (anat_ref_dimensions, anat_conform_xfm, [('t1w_valid_list', 'source_file')]), + (anat_ref_dimensions, anat_conform_xfm, [('anat_valid_list', 'source_file')]), (anat_conform, anat_conform_xfm, [('out_file', 'target_file')]), (anat_conform, n4_correct, [('out_file', 'input_image')]), (anat_conform, anat_merge, [ From aa7a43e353fe353447d96580e77a953a845c5c6b Mon Sep 17 00:00:00 2001 From: Chris Markiewicz Date: Thu, 25 Jul 2024 15:32:33 -0400 Subject: [PATCH 2/2] Update pyproject.toml Co-authored-by: Mathias Goncalves --- pyproject.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index 7bf5ae11aa..e8b8fbbc1f 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -25,7 +25,7 @@ dependencies = [ "matplotlib >= 2.2.0", "nibabel >= 4.0.1", "nipype >= 1.7.0", - "niworkflows @ git+https://github.com/nipreps/niworkflows.git@refs/pull/879/merge", + "niworkflows @ git+https://github.com/nipreps/niworkflows.git@master", "numpy", "packaging", "pybids >= 0.11.1",