RF: Replace InvertT1w with Rescale(invert=True)

Author: effigies

fmriprep/interfaces/__init__.py

@@ -5,7 +5,7 @@
     ReadSidecarJSON, DerivativesDataSink, BIDSDataGrabber, BIDSFreeSurferDir, BIDSInfo
 )
 from .images import (
-    IntraModalMerge, InvertT1w, ValidateImage, TemplateDimensions, Conform
+    IntraModalMerge, ValidateImage, TemplateDimensions, Conform
 )
 from .freesurfer import (
     StructuralReference, MakeMidthickness, FSInjectBrainExtracted,

fmriprep/interfaces/images.py

@@ -427,41 +427,6 @@ def _run_interface(self, runtime):
         return runtime
 
 
-class InvertT1wInputSpec(BaseInterfaceInputSpec):
-    in_file = File(exists=True, mandatory=True,
-                   desc='Skull-stripped T1w structural image')
-    ref_file = File(exists=True, mandatory=True,
-                    desc='Skull-stripped reference image')
-
-
-class InvertT1wOutputSpec(TraitedSpec):
-    out_file = File(exists=True, desc='Inverted T1w structural image')
-
-
-class InvertT1w(SimpleInterface):
-    input_spec = InvertT1wInputSpec
-    output_spec = InvertT1wOutputSpec
-
-    def _run_interface(self, runtime):
-        t1_img = nli.load_img(self.inputs.in_file)
-        t1_data = t1_img.get_data()
-        epi_data = nli.load_img(self.inputs.ref_file).get_data()
-
-        # We assume the image is already masked
-        mask = t1_data > 0
-
-        t1_min, t1_max = np.unique(t1_data)[[1, -1]]
-        epi_min, epi_max = np.unique(epi_data)[[1, -1]]
-        scale_factor = (epi_max - epi_min) / (t1_max - t1_min)
-
-        inv_data = mask * ((t1_max - t1_data) * scale_factor + epi_min)
-
-        out_file = fname_presuffix(self.inputs.in_file, suffix='_inv', newpath=runtime.cwd)
-        nli.new_img_like(t1_img, inv_data, copy_header=True).to_filename(out_file)
-        self._results['out_file'] = out_file
-        return runtime
-
-
 class DemeanImageInputSpec(BaseInterfaceInputSpec):
     in_file = File(exists=True, mandatory=True,
                    desc='image to be demeaned')

fmriprep/workflows/fieldmap/syn.py

@@ -28,9 +28,9 @@
 from nipype import logging
 from nipype.pipeline import engine as pe
 from nipype.interfaces import fsl, utility as niu
+from nipype.interfaces.image import Rescale
 from niworkflows.interfaces.fixes import (FixHeaderApplyTransforms as ApplyTransforms,
                                           FixHeaderRegistration as Registration)
-from ...interfaces import InvertT1w
 from ..bold.util import init_skullstrip_bold_wf
 
 DEFAULT_MEMORY_MIN_GB = 0.01
@@ -110,7 +110,7 @@ def init_syn_sdc_wf(omp_nthreads, bold_pe=None,
     affine_transform = pkgr.resource_filename('fmriprep', 'data/affine.json')
     syn_transform = pkgr.resource_filename('fmriprep', 'data/susceptibility_syn.json')
 
-    invert_t1w = pe.Node(InvertT1w(), name='invert_t1w',
+    invert_t1w = pe.Node(Rescale(invert=True), name='invert_t1w',
                          mem_gb=0.3)
 
     ref_2_t1 = pe.Node(Registration(from_file=affine_transform),