test: Compare nitransforms conversions to lta_convert/c3d_affine_tool

Author: effigies

fmriprep/interfaces/tests/test_nitransforms.py

@@ -0,0 +1,62 @@
+import nitransforms as nt
+import numpy as np
+from nibabel.tmpdirs import InGivenDirectory
+
+from fmriprep.interfaces import nitransforms as fin
+
+
+def test_ConvertAffine(tmp_path, data_dir):
+    bold = data_dir / 'sub-pixar008_task-pixar_desc-coreg_boldref.nii.gz'
+    anat = data_dir / 'sub-pixar008_desc-preproc_T1w.nii.gz'
+
+    # lta_affine = nt.linear.load(data_dir / 'mri_coreg.lta')
+    lta_convert_fsl = nt.linear.load(
+        data_dir / 'mri_coreg-lta_convert.mat', moving=bold, reference=anat, fmt='fsl'
+    )
+    lta_convert_itk = nt.linear.load(data_dir / 'mri_coreg-lta_convert.txt')
+    c3d_itk = nt.linear.load(data_dir / 'mri_coreg-c3d.txt')
+    lta_convert_itk_inv = nt.linear.load(data_dir / 'mri_coreg-lta_convert-invert.txt')
+    c3d_itk_inv = nt.linear.load(data_dir / 'mri_coreg-c3d-invert.txt')
+
+    with InGivenDirectory(tmp_path):
+        lta_to_fsl = fin.ConvertAffine(
+            in_xfm=data_dir / 'mri_coreg.lta',
+            reference=anat,
+            moving=bold,
+            out_fmt='fsl',
+        ).run()
+        assert lta_to_fsl.outputs.out_xfm == str(tmp_path / 'mri_coreg_fwd.mat')
+        assert not lta_to_fsl.outputs.out_inv
+
+        nitransforms_fsl = nt.linear.load(
+            lta_to_fsl.outputs.out_xfm, moving=bold, reference=anat, fmt='fsl'
+        )
+        assert np.allclose(nitransforms_fsl.matrix, lta_convert_fsl.matrix, atol=1e-4)
+
+        lta_to_itk = fin.ConvertAffine(in_xfm=data_dir / 'mri_coreg.lta', inverse=True).run()
+        assert lta_to_itk.outputs.out_xfm == str(tmp_path / 'mri_coreg_fwd.txt')
+        assert lta_to_itk.outputs.out_inv == str(tmp_path / 'mri_coreg_inv.txt')
+
+        nitransforms_itk = nt.linear.load(lta_to_itk.outputs.out_xfm)
+        assert np.allclose(nitransforms_itk.matrix, lta_convert_itk.matrix, atol=1e-4)
+        assert np.allclose(nitransforms_itk.matrix, c3d_itk.matrix, atol=1e-4)
+
+        nitransforms_itk_inv = nt.linear.load(lta_to_itk.outputs.out_inv)
+        assert np.allclose(nitransforms_itk_inv.matrix, lta_convert_itk_inv.matrix, atol=1e-4)
+        assert np.allclose(nitransforms_itk_inv.matrix, c3d_itk_inv.matrix, atol=1e-4)
+
+        fsl_to_itk = fin.ConvertAffine(
+            in_xfm=data_dir / 'mri_coreg-lta_convert.mat',
+            reference=anat,
+            moving=bold,
+            out_fmt='itk',
+            inverse=True,
+        ).run()
+
+        nitransforms_itk = nt.linear.load(fsl_to_itk.outputs.out_xfm)
+        assert np.allclose(nitransforms_itk.matrix, lta_convert_itk.matrix, atol=1e-4)
+        assert np.allclose(nitransforms_itk.matrix, c3d_itk.matrix, atol=1e-4)
+
+        nitransforms_itk_inv = nt.linear.load(fsl_to_itk.outputs.out_inv)
+        assert np.allclose(nitransforms_itk_inv.matrix, lta_convert_itk_inv.matrix, atol=1e-4)
+        assert np.allclose(nitransforms_itk_inv.matrix, c3d_itk_inv.matrix, atol=1e-4)