Merge pull request #930 from effigies/fix/cifti_shape

FIX: Set CIFTI-2 dimensions in the last three entries of ``dim``

Author: effigies

nibabel/cifti2/cifti2.py

@@ -1476,16 +1476,28 @@ def to_file_map(self, file_map=None):
     def update_headers(self):
         ''' Harmonize NIfTI headers with image data
 
+        Ensures that the NIfTI-2 header records the data shape in the last three
+        ``dim`` fields. Per the spec:
+
+            Because the first four dimensions in NIfTI are reserved for space and time, the CIFTI
+            dimensions are stored in the NIfTI header in dim[5] and up, where dim[5] is the length
+            of the first CIFTI dimension (number of values in a row), dim[6] is the length of the
+            second CIFTI dimension, and dim[7] is the length of the third CIFTI dimension, if
+            applicable. The fields dim[1] through dim[4] will be 1; dim[0] will be 6 or 7,
+            depending on whether a third matrix dimension exists.
+
         >>> import numpy as np
         >>> data = np.zeros((2,3,4))
         >>> img = Cifti2Image(data)
         >>> img.shape == (2, 3, 4)
         True
         >>> img.update_headers()
-        >>> img.nifti_header.get_data_shape() == (2, 3, 4)
+        >>> img.nifti_header.get_data_shape() == (1, 1, 1, 1, 2, 3, 4)
+        True
+        >>> img.shape == (2, 3, 4)
         True
         '''
-        self._nifti_header.set_data_shape(self._dataobj.shape)
+        self._nifti_header.set_data_shape((1, 1, 1, 1) + self._dataobj.shape)
 
     def get_data_dtype(self):
         return self._nifti_header.get_data_dtype()