diff --git a/aslprep/workflows/asl/outputs.py b/aslprep/workflows/asl/outputs.py index e0bb4001d..dc63588b1 100644 --- a/aslprep/workflows/asl/outputs.py +++ b/aslprep/workflows/asl/outputs.py @@ -191,6 +191,11 @@ def init_asl_derivatives_wf( "goodvoxels_mask", "surf_files", "surf_refs", + # Freesurfer outputs + "asl_aseg_t1", + "asl_aseg_std", + "asl_aparc_t1", + "asl_aparc_std", ], ), name="inputnode", @@ -486,7 +491,7 @@ def init_asl_derivatives_wf( # fmt:on if freesurfer: - ds_bold_aseg_t1 = pe.Node( + ds_asl_aseg_t1 = pe.Node( DerivativesDataSink( base_directory=config.execution.aslprep_dir, space="T1w", @@ -495,11 +500,11 @@ def init_asl_derivatives_wf( compress=True, dismiss_entities=("echo",), ), - name="ds_bold_aseg_t1", + name="ds_asl_aseg_t1", run_without_submitting=True, mem_gb=config.DEFAULT_MEMORY_MIN_GB, ) - ds_bold_aparc_t1 = pe.Node( + ds_asl_aparc_t1 = pe.Node( DerivativesDataSink( base_directory=config.execution.aslprep_dir, space="T1w", @@ -508,19 +513,19 @@ def init_asl_derivatives_wf( compress=True, dismiss_entities=("echo",), ), - name="ds_bold_aparc_t1", + name="ds_asl_aparc_t1", run_without_submitting=True, mem_gb=config.DEFAULT_MEMORY_MIN_GB, ) # fmt:off workflow.connect([ - (inputnode, ds_bold_aseg_t1, [ + (inputnode, ds_asl_aseg_t1, [ ("source_file", "source_file"), - ("bold_aseg_t1", "in_file"), + ("asl_aseg_t1", "in_file"), ]), - (inputnode, ds_bold_aparc_t1, [ + (inputnode, ds_asl_aparc_t1, [ ("source_file", "source_file"), - ("bold_aparc_t1", "in_file"), + ("asl_aparc_t1", "in_file"), ]), ]) # fmt:on @@ -585,12 +590,12 @@ def init_asl_derivatives_wf( if freesurfer: select_fs_std = pe.Node( - KeySelect(fields=["bold_aseg_std", "bold_aparc_std", "template"]), + KeySelect(fields=["asl_aseg_std", "asl_aparc_std", "template"]), name="select_fs_std", run_without_submitting=True, mem_gb=config.DEFAULT_MEMORY_MIN_GB, ) - ds_bold_aseg_std = pe.Node( + ds_asl_aseg_std = pe.Node( DerivativesDataSink( base_directory=config.execution.aslprep_dir, desc="aseg", @@ -598,11 +603,11 @@ def init_asl_derivatives_wf( compress=True, dismiss_entities=("echo",), ), - name="ds_bold_aseg_std", + name="ds_asl_aseg_std", run_without_submitting=True, mem_gb=config.DEFAULT_MEMORY_MIN_GB, ) - ds_bold_aparc_std = pe.Node( + ds_asl_aparc_std = pe.Node( DerivativesDataSink( base_directory=config.execution.aslprep_dir, desc="aparcaseg", @@ -610,7 +615,7 @@ def init_asl_derivatives_wf( compress=True, dismiss_entities=("echo",), ), - name="ds_bold_aparc_std", + name="ds_asl_aparc_std", run_without_submitting=True, mem_gb=config.DEFAULT_MEMORY_MIN_GB, ) @@ -618,27 +623,27 @@ def init_asl_derivatives_wf( workflow.connect([ (spacesource, select_fs_std, [("uid", "key")]), (inputnode, select_fs_std, [ - ("bold_aseg_std", "bold_aseg_std"), - ("bold_aparc_std", "bold_aparc_std"), + ("asl_aseg_std", "asl_aseg_std"), + ("asl_aparc_std", "asl_aparc_std"), ("template", "template"), ("spatial_reference", "keys"), ]), - (select_fs_std, ds_bold_aseg_std, [("bold_aseg_std", "in_file")]), - (spacesource, ds_bold_aseg_std, [ + (select_fs_std, ds_asl_aseg_std, [("asl_aseg_std", "in_file")]), + (spacesource, ds_asl_aseg_std, [ ("space", "space"), ("cohort", "cohort"), ("resolution", "resolution"), ("density", "density"), ]), - (select_fs_std, ds_bold_aparc_std, [("bold_aparc_std", "in_file")]), - (spacesource, ds_bold_aparc_std, [ + (select_fs_std, ds_asl_aparc_std, [("asl_aparc_std", "in_file")]), + (spacesource, ds_asl_aparc_std, [ ("space", "space"), ("cohort", "cohort"), ("resolution", "resolution"), ("density", "density"), ]), - (inputnode, ds_bold_aseg_std, [("source_file", "source_file")]), - (inputnode, ds_bold_aparc_std, [("source_file", "source_file")]) + (inputnode, ds_asl_aseg_std, [("source_file", "source_file")]), + (inputnode, ds_asl_aparc_std, [("source_file", "source_file")]) ]) # fmt:on @@ -662,14 +667,14 @@ def init_asl_derivatives_wf( run_without_submitting=True, ) - ds_bold_surfs = pe.MapNode( + ds_asl_surfs = pe.MapNode( DerivativesDataSink( base_directory=config.execution.aslprep_dir, extension=".func.gii", TaskName=metadata.get("TaskName"), ), iterfield=["in_file", "hemi"], - name="ds_bold_surfs", + name="ds_asl_surfs", run_without_submitting=True, mem_gb=config.DEFAULT_MEMORY_MIN_GB, ) @@ -680,12 +685,12 @@ def init_asl_derivatives_wf( ("surf_refs", "keys"), ]), (select_fs_surf, name_surfs, [("surfaces", "in_file")]), - (inputnode, ds_bold_surfs, [("source_file", "source_file")]), - (select_fs_surf, ds_bold_surfs, [ + (inputnode, ds_asl_surfs, [("source_file", "source_file")]), + (select_fs_surf, ds_asl_surfs, [ ("surfaces", "in_file"), ("key", "space"), ]), - (name_surfs, ds_bold_surfs, [("hemi", "hemi")]), + (name_surfs, ds_asl_surfs, [("hemi", "hemi")]), ]) # fmt:on @@ -715,22 +720,22 @@ def init_asl_derivatives_wf( # CIFTI output if cifti_output: - ds_bold_cifti = pe.Node( + ds_asl_cifti = pe.Node( DerivativesDataSink( base_directory=config.execution.aslprep_dir, - suffix="bold", + suffix="asl", compress=False, TaskName=metadata.get("TaskName"), space="fsLR", ), - name="ds_bold_cifti", + name="ds_asl_cifti", run_without_submitting=True, mem_gb=config.DEFAULT_MEMORY_MIN_GB, ) # fmt:off workflow.connect([ - (inputnode, ds_bold_cifti, [ - ("bold_cifti", "in_file"), + (inputnode, ds_asl_cifti, [ + ("asl_cifti", "in_file"), ("source_file", "source_file"), ("cifti_density", "density"), (("cifti_metadata", _read_json), "meta_dict"),