fix zooms if difference between zooms and target zooms is between 0.01 and 0.001 mm

Author: fliem

niworkflows/interfaces/images.py

@@ -306,17 +306,23 @@ def _run_interface(self, runtime):
 
         # Set a 0.01mm threshold to performing rescaling
         atol = {"meter": 1e-5, "mm": 0.01, "micron": 10}[xyz_unit]
+        # if 0.01 > difference > 0.001mm, freesurfer won't be able to merge the images
+        atol_fine = {"meter": 1e-6, "mm": 0.001, "micron": 1}[xyz_unit]
 
         # Rescale => change zooms
+        # Fix zooms => set zooms without changing affine
         # Resize => update image dimensions
         rescale = not np.allclose(zooms, target_zooms, atol=atol)
+        fix_zooms = not np.allclose(zooms, target_zooms, atol=atol_fine)
         resize = not np.all(shape == target_shape)
-        if rescale or resize:
+        if rescale or resize or fix_zooms:
             if rescale:
                 scale_factor = target_zooms / zooms
                 target_affine[:3, :3] = reoriented.affine[:3, :3].dot(
                     np.diag(scale_factor)
                 )
+            elif fix_zooms:
+                reoriented.header.set_zooms(target_zooms)
 
             if resize:
                 # The shift is applied after scaling.

niworkflows/interfaces/tests/test_images.py

@@ -180,3 +180,35 @@ def test_IntraModalMerge(tmpdir, shape, mshape):
     merged_data = nb.load(merged).get_fdata(dtype="float32")
     new_mshape = (*mshape[:3], 2 if len(mshape) == 3 else mshape[3] * 2)
     assert merged_data.shape == new_mshape
+
+
+def test_conform_resize(tmpdir):
+    fname = str(tmpdir / "test.nii")
+
+    random_data = np.random.random(size=(5, 5, 5))
+    img = nb.Nifti1Image(random_data, np.eye(4))
+    img.to_filename(fname)
+    conform = pe.Node(im.Conform(), name="conform", base_dir=str(tmpdir))
+    conform.inputs.in_file = fname
+    conform.inputs.target_zooms = (1, 1, 1.5)
+    conform.inputs.target_shape = (5, 5, 5)
+    res = conform.run()
+
+    out_img = nb.load(res.outputs.out_file)
+    assert out_img.header.get_zooms() == conform.inputs.target_zooms
+
+
+def test_conform_set_zooms(tmpdir):
+    fname = str(tmpdir / "test.nii")
+
+    random_data = np.random.random(size=(5, 5, 5))
+    img = nb.Nifti1Image(random_data, np.eye(4))
+    img.to_filename(fname)
+    conform = pe.Node(im.Conform(), name="conform", base_dir=str(tmpdir))
+    conform.inputs.in_file = fname
+    conform.inputs.target_zooms = (1, 1, 1.002)
+    conform.inputs.target_shape = (5, 5, 5)
+    res = conform.run()
+
+    out_img = nb.load(res.outputs.out_file)
+    assert np.allclose(out_img.header.get_zooms(), conform.inputs.target_zooms)