RF: Use nipype.interfaces.image.Reorient

Author: effigies

fmriprep/interfaces/__init__.py

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

fmriprep/interfaces/images.py

@@ -291,52 +291,6 @@ def _run_interface(self, runtime):
         return runtime
 
 
-class ReorientInputSpec(BaseInterfaceInputSpec):
-    in_file = File(exists=True, mandatory=True,
-                   desc='Input T1w image')
-
-
-class ReorientOutputSpec(TraitedSpec):
-    out_file = File(exists=True, desc='Reoriented T1w image')
-    transform = File(exists=True, desc='Reorientation transform')
-
-
-class Reorient(SimpleInterface):
-    """Reorient a T1w image to RAS (left-right, posterior-anterior, inferior-superior)
-
-    Syncs qform and sform codes for consistent treatment by all software
-    """
-    input_spec = ReorientInputSpec
-    output_spec = ReorientOutputSpec
-
-    def _run_interface(self, runtime):
-        # Load image, orient as RAS
-        fname = self.inputs.in_file
-        orig_img = nb.load(fname)
-        reoriented = nb.as_closest_canonical(orig_img)
-
-        # Reconstruct transform from orig to reoriented image
-        ornt_xfm = nb.orientations.inv_ornt_aff(
-            nb.io_orientation(orig_img.affine), orig_img.shape)
-
-        normalized = normalize_xform(reoriented)
-
-        # Image may be reoriented
-        if normalized is not orig_img:
-            out_name = fname_presuffix(fname, suffix='_ras', newpath=runtime.cwd)
-            normalized.to_filename(out_name)
-        else:
-            out_name = fname
-
-        mat_name = fname_presuffix(fname, suffix='.mat', newpath=runtime.cwd, use_ext=False)
-        np.savetxt(mat_name, ornt_xfm, fmt='%.08f')
-
-        self._results['out_file'] = out_name
-        self._results['transform'] = mat_name
-
-        return runtime
-
-
 class ValidateImageInputSpec(BaseInterfaceInputSpec):
     in_file = File(exists=True, mandatory=True, desc='input image')
 

fmriprep/workflows/anatomical.py

@@ -30,7 +30,8 @@
     utility as niu,
     c3,
     freesurfer as fs,
-    fsl
+    fsl,
+    image,
 )
 from nipype.interfaces.ants import BrainExtraction, N4BiasFieldCorrection
 
@@ -43,7 +44,7 @@
 
 from ..interfaces import (
     DerivativesDataSink, MakeMidthickness, FSInjectBrainExtracted,
-    FSDetectInputs, NormalizeSurf, GiftiNameSource, TemplateDimensions, Conform, Reorient,
+    FSDetectInputs, NormalizeSurf, GiftiNameSource, TemplateDimensions, Conform,
     ConcatAffines, RefineBrainMask,
 )
 from ..utils.misc import fix_multi_T1w_source_name, add_suffix
@@ -481,7 +482,7 @@ def _get_first(in_list):
         name='t1_merge')
 
     # 2. Reorient template to RAS, if needed (mri_robust_template may set to LIA)
-    t1_reorient = pe.Node(Reorient(), name='t1_reorient')
+    t1_reorient = pe.Node(image.Reorient(), name='t1_reorient')
 
     lta_to_fsl = pe.MapNode(fs.utils.LTAConvert(out_fsl=True), iterfield=['in_lta'],
                             name='lta_to_fsl')