Use GenericLabel and set nprocs.

src/fmripost_rapidtide/interfaces/misc.py

@@ -0,0 +1,54 @@
+"""Miscellaneous interfaces for fmriprep-rapidtide."""
+
+from nipype.interfaces.base import (
+    isdefined,
+    traits,
+)
+from nipype.utils.filemanip import fname_presuffix
+from niworkflows.interfaces.fixes import (
+    FixHeaderApplyTransforms,
+    _FixTraitApplyTransformsInputSpec,
+)
+
+
+class _ApplyTransformsInputSpec(_FixTraitApplyTransformsInputSpec):
+    # Nipype's version doesn't have GenericLabel
+    interpolation = traits.Enum(
+        'Linear',
+        'NearestNeighbor',
+        'CosineWindowedSinc',
+        'WelchWindowedSinc',
+        'HammingWindowedSinc',
+        'LanczosWindowedSinc',
+        'MultiLabel',
+        'Gaussian',
+        'BSpline',
+        'GenericLabel',
+        argstr='%s',
+        usedefault=True,
+    )
+
+
+class ApplyTransforms(FixHeaderApplyTransforms):
+    """A modified version of FixHeaderApplyTransforms from niworkflows.
+
+    The niworkflows version of ApplyTransforms "fixes the resampled image header
+    to match the xform of the reference image".
+    This modification overrides the allowed interpolation values,
+    since FixHeaderApplyTransforms doesn't support GenericLabel,
+    which is preferred over MultiLabel.
+    """
+
+    input_spec = _ApplyTransformsInputSpec
+
+    def _run_interface(self, runtime):
+        if not isdefined(self.inputs.output_image):
+            self.inputs.output_image = fname_presuffix(
+                self.inputs.input_image,
+                suffix='_trans.nii.gz',
+                newpath=runtime.cwd,
+                use_ext=False,
+            )
+
+        runtime = super(ApplyTransforms, self)._run_interface(runtime)
+        return runtime

src/fmripost_rapidtide/interfaces/rapidtide.py

@@ -252,6 +252,12 @@ class _RapidtideInputSpec(CommandLineInputSpec):
         argstr='--autorespdelete',
         mandatory=False,
     )
+    nprocs = traits.Int(
+        default=1,
+        usedefault=True,
+        argstr='--nprocs %d',
+        mandatory=False,
+    )
 
 
 class _RapidtideOutputSpec(TraitedSpec):

src/fmripost_rapidtide/workflows/base.py

@@ -391,10 +391,11 @@ def init_single_run_wf(bold_file):
         # Resample to MNI152NLin6Asym:res-2, for rapidtide denoising
         from fmriprep.workflows.bold.apply import init_bold_volumetric_resample_wf
         from fmriprep.workflows.bold.stc import init_bold_stc_wf
-        from niworkflows.interfaces.fixes import FixHeaderApplyTransforms as ApplyTransforms
         from niworkflows.interfaces.header import ValidateImage
         from templateflow.api import get as get_template
 
+        from fmripost_rapidtide.interfaces.misc import ApplyTransforms
+
         workflow.__desc__ += """\
 Raw BOLD series were resampled to MNI152NLin6Asym:res-2, for rapidtide denoising.
 """

src/fmripost_rapidtide/workflows/confounds.py

@@ -82,12 +82,12 @@ def init_carpetplot_wf(
     from nipype.interfaces import utility as niu
     from nipype.pipeline import engine as pe
     from niworkflows.engine.workflows import LiterateWorkflow as Workflow
-    from niworkflows.interfaces.fixes import FixHeaderApplyTransforms as ApplyTransforms
     from templateflow.api import get as get_template
 
     from fmripost_rapidtide.config import DEFAULT_MEMORY_MIN_GB
     from fmripost_rapidtide.interfaces import DerivativesDataSink
     from fmripost_rapidtide.interfaces.confounds import FMRISummary
+    from fmripost_rapidtide.interfaces.misc import ApplyTransforms
 
     inputnode = pe.Node(
         niu.IdentityInterface(

src/fmripost_rapidtide/workflows/outputs.py

@@ -27,11 +27,11 @@
 from fmriprep.utils.bids import dismiss_echo
 from nipype.interfaces import utility as niu
 from nipype.pipeline import engine as pe
-from niworkflows.interfaces.fixes import FixHeaderApplyTransforms as ApplyTransforms
 from niworkflows.utils.images import dseg_label
 
 from fmripost_rapidtide.config import DEFAULT_MEMORY_MIN_GB
 from fmripost_rapidtide.interfaces.bids import DerivativesDataSink
+from fmripost_rapidtide.interfaces.misc import ApplyTransforms
 
 
 def init_func_fit_reports_wf(

src/fmripost_rapidtide/workflows/rapidtide.py

@@ -135,7 +135,6 @@ def init_rapidtide_wf(
     rapidtide = pe.Node(
         Rapidtide(
             outputname='rapidtide',
-            denoising=True,
             datatstep=metadata['RepetitionTime'],
             autosync=config.workflow.autosync,
             filterband=config.workflow.filterband,
@@ -169,9 +168,11 @@ def init_rapidtide_wf(
             outputlevel=config.workflow.outputlevel,
             territorymap=config.workflow.territorymap or Undefined,
             autorespdelete=config.workflow.autorespdelete,
+            nprocs=config.nipype.omp_nthreads,
         ),
         name='rapidtide',
         mem_gb=mem_gb['largemem'],
+        n_procs=config.nipype.omp_nthreads,
     )
     workflow.connect([
         (inputnode, rapidtide, [