diff --git a/aslprep/tests/test_cli.py b/aslprep/tests/test_cli.py index 3acd5328a..a2b432bb3 100644 --- a/aslprep/tests/test_cli.py +++ b/aslprep/tests/test_cli.py @@ -355,7 +355,7 @@ def test_test_003_full(data_dir, output_dir, working_dir): output_dir, working_dir, level='full', - extra_params=['--cifti-output', '91k'], + extra_params=['--cifti-output', '91k', '--project-goodvoxels'], ) diff --git a/aslprep/workflows/asl/base.py b/aslprep/workflows/asl/base.py index 6c5fbdbb1..b0c195abf 100644 --- a/aslprep/workflows/asl/base.py +++ b/aslprep/workflows/asl/base.py @@ -770,7 +770,6 @@ def init_asl_wf( ds_asl_cifti_wf.inputs.inputnode.source_files = [asl_file] workflow.connect([ (inputnode, ds_asl_cifti_wf, [ - ('t1w_preproc', 'inputnode.anat'), ('mni6_mask', 'inputnode.mni6_mask'), ('anat2mni6_xfm', 'inputnode.anat2mni6_xfm'), ('white', 'inputnode.white'), @@ -780,6 +779,10 @@ def init_asl_wf( ('sphere_reg_fsLR', 'inputnode.sphere_reg_fsLR'), ('cortex_mask', 'inputnode.cortex_mask'), ]), + (asl_anat_wf, ds_asl_cifti_wf, [ + # Used for affine/resolution reference only + ('outputnode.resampling_reference', 'inputnode.anat_ref_file'), + ]), (asl_fit_wf, ds_asl_cifti_wf, [ ('outputnode.aslref2anat_xfm', 'inputnode.aslref2anat_xfm'), ]), diff --git a/aslprep/workflows/asl/outputs.py b/aslprep/workflows/asl/outputs.py index d222fe56c..285bb882c 100644 --- a/aslprep/workflows/asl/outputs.py +++ b/aslprep/workflows/asl/outputs.py @@ -837,11 +837,12 @@ def init_ds_ciftis_wf( inputnode_fields = [ 'asl_cifti', 'source_files', - # Anatomical - 'anat', + # ASL-resolution, anatomical-space reference image + 'anat_ref_file', 'aslref2anat_xfm', # Template 'anat2mni6_xfm', + # Template reference image. Resolution depends on CIFTI output resolution 'mni6_mask', # Pre-computed goodvoxels mask. May be Undefined. 'goodvoxels_mask', @@ -927,7 +928,7 @@ def init_ds_ciftis_wf( workflow.connect([ (inputnode, warp_cbf_to_anat, [ (cbf_deriv, 'input_image'), - ('anat', 'reference_image'), + ('anat_ref_file', 'reference_image'), ('aslref2anat_xfm', 'transforms'), ]), ]) # fmt:skip