fix(interface): EstimateReferenceImage generates 4D references if…

… 4D SBRefs are supplied as input.

This patch checks the dimensionality of SBRefs and generates an average if the SBRef is 4D.
Fixes nipreps/fmriprep#1579.
Intimately related to nipreps#253, although I'm not sure the proposed resampling there is absolutely necessary.
It could be detrimental for ``bbregister`` in co-registration.
It is very likely necessary for head-motion correction with either ``mcflirt`` or ``3dVolReg``.

niworkflows/interfaces/registration.py

@@ -370,45 +370,55 @@ class EstimateReferenceImage(SimpleInterface):
     output_spec = EstimateReferenceImageOutputSpec
 
     def _run_interface(self, runtime):
-        in_nii = nb.load(self.inputs.in_file)
-        n_volumes_to_discard = _get_vols_to_discard(in_nii)
+        ref_name = self.inputs.in_file
+        ref_nii = nb.load(ref_name)
+        n_volumes_to_discard = _get_vols_to_discard(ref_nii)
 
         self._results["n_volumes_to_discard"] = n_volumes_to_discard
 
+        out_ref_fname = os.path.join(runtime.cwd, "ref_bold.nii.gz")
         if isdefined(self.inputs.sbref_file):
-            self._results['ref_image'] = self.inputs.sbref_file
-            return runtime
+            out_ref_fname = os.path.join(runtime.cwd, "ref_sbref.nii.gz")
+            ref_name = self.inputs.sbref_file
+            ref_nii = nb.squeeze_image(nb.load(ref_name))
+
+            # If reference is only 1 volume, return it directly
+            if ref_nii.get_data().ndim == 3:
+                ref_nii.header.extensions.clear()
+                ref_nii.to_filename(out_ref_fname)
+                self._results['ref_image'] = out_ref_fname
+                return runtime
+            else:
+                # Reset this variable as it no longer applies
+                # and value for the output is stored in self._results
+                n_volumes_to_discard = 0
 
         # Slicing may induce inconsistencies with shape-dependent values in extensions.
         # For now, remove all. If this turns out to be a mistake, we can select extensions
         # that don't break pipeline stages.
-        in_nii.header.extensions.clear()
-
-        out_ref_fname = os.path.join(runtime.cwd, "ref_image.nii.gz")
+        ref_nii.header.extensions.clear()
 
         if n_volumes_to_discard == 0:
-            if in_nii.shape[-1] > 40:
-                slice_fname = os.path.join(runtime.cwd, "slice.nii.gz")
-                nb.Nifti1Image(in_nii.dataobj[:, :, :, 20:40], in_nii.affine,
-                               in_nii.header).to_filename(slice_fname)
-            else:
-                slice_fname = self.inputs.in_file
+            if ref_nii.shape[-1] > 40:
+                ref_name = os.path.join(runtime.cwd, "slice.nii.gz")
+                nb.Nifti1Image(ref_nii.dataobj[:, :, :, 20:40], ref_nii.affine,
+                               ref_nii.header).to_filename(ref_name)
 
             if self.inputs.mc_method == "AFNI":
-                res = afni.Volreg(in_file=slice_fname, args='-Fourier -twopass',
+                res = afni.Volreg(in_file=ref_name, args='-Fourier -twopass',
                                   zpad=4, outputtype='NIFTI_GZ').run()
             elif self.inputs.mc_method == "FSL":
-                res = fsl.MCFLIRT(in_file=slice_fname,
+                res = fsl.MCFLIRT(in_file=ref_name,
                                   ref_vol=0, interpolation='sinc').run()
             mc_slice_nii = nb.load(res.outputs.out_file)
 
             median_image_data = np.median(mc_slice_nii.get_data(), axis=3)
         else:
             median_image_data = np.median(
-                in_nii.dataobj[:, :, :, :n_volumes_to_discard], axis=3)
+                ref_nii.dataobj[:, :, :, :n_volumes_to_discard], axis=3)
 
-        nb.Nifti1Image(median_image_data, in_nii.affine,
-                       in_nii.header).to_filename(out_ref_fname)
+        nb.Nifti1Image(median_image_data, ref_nii.affine,
+                       ref_nii.header).to_filename(out_ref_fname)
 
         self._results["ref_image"] = out_ref_fname