new way to deoblique

Author: chrisgorgo

fmriprep/interfaces/images.py

@@ -293,6 +293,7 @@ def _run_interface(self, runtime):
 
 class ValidateImageInputSpec(BaseInterfaceInputSpec):
     in_file = File(exists=True, mandatory=True, desc='input image')
+    deoblique = traits.Bool(False, usedefault=True)
 
 
 class ValidateImageOutputSpec(TraitedSpec):
@@ -342,6 +343,15 @@ class ValidateImage(SimpleInterface):
     output_spec = ValidateImageOutputSpec
 
     def _run_interface(self, runtime):
+
+        def deoblique(img):
+            import os
+            import nibabel as nb
+            import numpy as np
+            affine = img.affine
+            affine[:3, :3] = np.diag(np.diag(affine[:3, :3]))
+            return nb.Nifti1Image(np.asanyarray(img.dataobj), affine, img.header)
+
         img = nb.load(self.inputs.in_file)
         out_report = os.path.join(runtime.cwd, 'report.html')
 
@@ -370,7 +380,13 @@ def _run_interface(self, runtime):
 
         # Both match, qform valid (implicit with match), codes okay -> do nothing, empty report
         if matching_affines and qform_code > 0 and sform_code > 0:
-            self._results['out_file'] = self.inputs.in_file
+            if self.inputs.deoblique:
+                out_fname = fname_presuffix(self.inputs.in_file, suffix='_valid', newpath=runtime.cwd)
+                img = deoblique(img)
+                img.to_filename(out_fname)
+                self._results['out_file'] = out_fname
+            else:
+                self._results['out_file'] = self.inputs.in_file
             open(out_report, 'w').close()
             self._results['out_report'] = out_report
             return runtime
@@ -418,6 +434,9 @@ def _run_interface(self, runtime):
 </p>
 """
         snippet = '<h3 class="elem-title">%s</h3>\n%s\n' % (warning_txt, description)
+
+        if self.inputs.deoblique:
+            img = deoblique(img)
         # Store new file and report
         img.to_filename(out_fname)
         with open(out_report, 'w') as fobj:

fmriprep/workflows/bold/util.py

@@ -103,9 +103,8 @@ def init_bold_reference_wf(omp_nthreads, bold_file=None, name='bold_reference_wf
 
     gen_ref = pe.Node(EstimateReferenceImage(), name="gen_ref",
                       mem_gb=1)  # OE: 128x128x128x50 * 64 / 8 ~ 900MB.
-    deoblique = pe.Node(afni.Refit(deoblique=True), name='deoblique')
     # Re-run validation; no effect if no sbref; otherwise apply same validation to sbref as bold
-    validate_ref = pe.Node(ValidateImage(), name='validate_ref', mem_gb=DEFAULT_MEMORY_MIN_GB)
+    validate_ref = pe.Node(ValidateImage(deoblique=True), name='validate_ref', mem_gb=DEFAULT_MEMORY_MIN_GB)
     enhance_and_skullstrip_bold_wf = init_enhance_and_skullstrip_bold_wf(omp_nthreads=omp_nthreads)
 
     workflow.connect([