diff --git a/xcp_d/interfaces/ants.py b/xcp_d/interfaces/ants.py index 86f075790..ccd6352af 100644 --- a/xcp_d/interfaces/ants.py +++ b/xcp_d/interfaces/ants.py @@ -25,7 +25,7 @@ class _ConvertTransformFileInputSpec(CommandLineInputSpec): - dimension = traits.Enum((3, 2), default=3, usedefault=True, argstr="%d", position=0) + dimension = traits.Enum(3, 2, usedefault=True, argstr="%d", position=0) in_transform = traits.File(exists=True, argstr="%s", mandatory=True, position=1) out_transform = traits.File( argstr="%s", diff --git a/xcp_d/interfaces/bids.py b/xcp_d/interfaces/bids.py index c81a81da4..ee5ef316e 100644 --- a/xcp_d/interfaces/bids.py +++ b/xcp_d/interfaces/bids.py @@ -312,7 +312,7 @@ class _BIDSURIInputSpec(DynamicTraitedSpec): out_dir = traits.Str(mandatory=True, desc="Output directory") metadata = traits.Dict(desc="Metadata dictionary") field = traits.Str( - default="Sources", + "Sources", usedefault=True, desc="Field to use for BIDS URIs in metadata dict", ) diff --git a/xcp_d/interfaces/censoring.py b/xcp_d/interfaces/censoring.py index 3f6a32677..c58985e56 100644 --- a/xcp_d/interfaces/censoring.py +++ b/xcp_d/interfaces/censoring.py @@ -215,7 +215,7 @@ class _CensorInputSpec(BaseInterfaceInputSpec): ), ) column = traits.Str( - default="framewise_displacement", + "framewise_displacement", usedefault=True, mandatory=False, desc="Column name in the temporal mask to use for censoring.", diff --git a/xcp_d/interfaces/connectivity.py b/xcp_d/interfaces/connectivity.py index 430a597b7..2717b5ff2 100644 --- a/xcp_d/interfaces/connectivity.py +++ b/xcp_d/interfaces/connectivity.py @@ -31,7 +31,7 @@ class _NiftiParcellateInputSpec(BaseInterfaceInputSpec): atlas = File(exists=True, mandatory=True, desc="atlas file") atlas_labels = File(exists=True, mandatory=True, desc="atlas labels file") min_coverage = traits.Float( - default=0.5, + 0.5, usedefault=True, desc=( "Coverage threshold to apply to parcels. " diff --git a/xcp_d/interfaces/plotting.py b/xcp_d/interfaces/plotting.py index d7f4dfcc6..fdb6660d3 100644 --- a/xcp_d/interfaces/plotting.py +++ b/xcp_d/interfaces/plotting.py @@ -529,7 +529,6 @@ class _SlicesDirInputSpec(FSLCommandInputSpec): out_extension = traits.Enum( (".gif", ".png", ".svg"), - default=".gif", usedefault=True, desc="Convenience parameter to let xcp_d select the extension.", ) @@ -670,10 +669,10 @@ class _PlotCiftiParcellationInputSpec(BaseInterfaceInputSpec): desc="Labels for the CIFTI files.", ) out_file = File( + "plot.svg", exists=False, mandatory=False, desc="Output file.", - default="plot.svg", usedefault=True, ) vmin = traits.Float( diff --git a/xcp_d/interfaces/workbench.py b/xcp_d/interfaces/workbench.py index 98747845d..557c5773a 100644 --- a/xcp_d/interfaces/workbench.py +++ b/xcp_d/interfaces/workbench.py @@ -622,7 +622,7 @@ class _CiftiParcellateWorkbenchInputSpec(_WBCommandInputSpec): "MODE", "COUNT_NONZERO", position=12, - default="MEAN", + usedefault=True, argstr="-method %s", desc="Specify method of parcellation (default MEAN, or MODE if label data)", ) @@ -709,7 +709,7 @@ class _CiftiSurfaceResampleInputSpec(_WBCommandInputSpec): "The BARYCENTRIC method is generally recommended for anatomical surfaces, " "in order to minimize smoothing." ), - default="BARYCENTRIC", + usedefault=True, ) out_file = File( name_source=["in_file"], diff --git a/xcp_d/workflows/bold/outputs.py b/xcp_d/workflows/bold/outputs.py index 1add059f5..c919e36a3 100644 --- a/xcp_d/workflows/bold/outputs.py +++ b/xcp_d/workflows/bold/outputs.py @@ -615,7 +615,7 @@ def init_postproc_derivatives_wf( run_without_submitting=True, mem_gb=1, name="make_ccorrs_meta_dict2", - iterfield=["in1"], + iterfield=["in1", "metadata"], ) workflow.connect([ (inputnode, make_ccorrs_meta_dict2, [("atlas_files", "in1")]),