Merge pull request #1059 from vanandrew/cifti_fix

FIX: Reshape CIFTI-2 affines to 4x4 when encoded as row-major sequence

Author: effigies

nibabel/cifti2/parse_cifti2.py

@@ -538,7 +538,8 @@ def flush_chardata(self):
             # conversion to numpy array
             c = BytesIO(data.strip().encode('utf-8'))
             transform = self.struct_state[-1]
-            transform.matrix = np.loadtxt(c, dtype=np.float64)
+            matrix = np.loadtxt(c, dtype=np.float64)
+            transform.matrix = matrix.reshape(4, 4)
             c.close()
 
         elif self.write_to == 'Label':

nibabel/cifti2/tests/test_cifti2io_header.py

@@ -41,6 +41,11 @@
 datafiles = [DATA_FILE2, DATA_FILE3, DATA_FILE4, DATA_FILE5, DATA_FILE6]
 
 
+def test_space_separated_affine():
+    img = ci.Cifti2Image.from_filename(
+        pjoin(NIBABEL_TEST_DATA, "row_major.dconn.nii"))
+
+
 def test_read_nifti2():
     # Error trying to read a CIFTI-2 image from a NIfTI2-only image.
     filemap = ci.Cifti2Image.make_file_map()