Merge pull request #315 from effigies/ico7

MRG: Automatically reshape FreeSurfer ico7 niftis

Tried to follow in the footsteps of f53c168. Presents programmer with data object equivalent to an MGH, leaving header intact for writing to file.

Author: matthew-brett

nibabel-data/nitest-freesurfer

@@ -698,16 +698,26 @@ def get_data_shape(self):
         Allows for freesurfer hack for large vectors described in
         https://github.com/nipy/nibabel/issues/100 and
         https://code.google.com/p/fieldtrip/source/browse/trunk/external/freesurfer/save_nifti.m?spec=svn5022&r=5022#77
+
+        Allows for freesurfer hack for 7th order icosahedron surface described
+        in
+        https://github.com/nipy/nibabel/issues/309
+        https://code.google.com/p/fieldtrip/source/browse/trunk/external/freesurfer/load_nifti.m?r=8776#86
+        https://code.google.com/p/fieldtrip/source/browse/trunk/external/freesurfer/save_nifti.m?r=8776#50
         '''
         shape = super(Nifti1Header, self).get_data_shape()
         # Apply freesurfer hack for vector
-        if shape != (-1, 1, 1): # Normal case
+        if shape == (-1, 1, 1):
+            vec_len = int(self._structarr['glmin'])
+            if vec_len == 0:
+                raise HeaderDataError('-1 in dim[1] but 0 in glmin; '
+                                      'inconsistent freesurfer type header?')
+            return (vec_len, 1, 1)
+        # Apply freesurfer hack for ico7 surface
+        elif shape == (27307, 1, 6):
+            return (163842, 1, 1)
+        else:  # Normal case
             return shape
-        vec_len = int(self._structarr['glmin'])
-        if vec_len == 0:
-            raise HeaderDataError('-1 in dim[1] but 0 in glmin; inconsistent '
-                                  'freesurfer type header?')
-        return (vec_len, 1, 1)
 
     def set_data_shape(self, shape):
         ''' Set shape of data
@@ -725,12 +735,22 @@ def set_data_shape(self, shape):
         Applies freesurfer hack for large vectors described in
         https://github.com/nipy/nibabel/issues/100 and
         https://code.google.com/p/fieldtrip/source/browse/trunk/external/freesurfer/save_nifti.m?spec=svn5022&r=5022#77
+
+        Allows for freesurfer hack for 7th order icosahedron surface described
+        in
+        https://github.com/nipy/nibabel/issues/309
+        https://code.google.com/p/fieldtrip/source/browse/trunk/external/freesurfer/load_nifti.m?r=8776#86
+        https://code.google.com/p/fieldtrip/source/browse/trunk/external/freesurfer/save_nifti.m?r=8776#50
         '''
-        # Apply freesurfer hack for vector
         hdr = self._structarr
         shape = tuple(shape)
-        if (len(shape) == 3 and shape[1:] == (1, 1) and
-            shape[0] > np.iinfo(hdr['dim'].dtype.base).max): # Freesurfer case
+
+        # Apply freesurfer hack for ico7 surface
+        if shape == (163842, 1, 1):
+            shape = (27307, 1, 6)
+        # Apply freesurfer hack for vector
+        elif (len(shape) == 3 and shape[1:] == (1, 1) and
+                shape[0] > np.iinfo(hdr['dim'].dtype.base).max):
             try:
                 hdr['glmin'] = shape[0]
             except OverflowError:

nibabel/nifti1.py

@@ -24,8 +24,11 @@
                       Nifti1Pair, Nifti1Extension, Nifti1Extensions,
                       data_type_codes, extension_codes, slice_order_codes)
 
+from ..freesurfer import load as mghload
+
 from .test_arraywriters import rt_err_estimate, IUINT_TYPES
 from .test_helpers import bytesio_filemap, bytesio_round_trip
+from .nibabel_data import get_nibabel_data, needs_nibabel_data
 
 from numpy.testing import (assert_array_equal, assert_array_almost_equal,
                            assert_almost_equal)
@@ -242,7 +245,7 @@ def test_magic_offset_checks(self):
                      'file nifti1; setting to minimum value '
                      'of ' + str(hdr.single_vox_offset))
 
-    def test_freesurfer_hack(self):
+    def test_freesurfer_large_vector_hack(self):
         # For large vector images, Freesurfer appears to set dim[1] to -1 and
         # then use glmin for the vector length (an i4)
         HC = self.header_class
@@ -288,6 +291,31 @@ def test_freesurfer_hack(self):
                     hdr.set_data_shape(constructor(shape))
                 assert_equal(hdr.get_data_shape(), shape)
 
+    @needs_nibabel_data('nitest-freesurfer')
+    def test_freesurfer_ico7_hack(self):
+        HC = self.header_class
+        hdr = HC()
+        # Test that using ico7 shape automatically uses factored dimensions
+        hdr.set_data_shape((163842, 1, 1))
+        assert_array_equal(hdr._structarr['dim'][1:4], np.array([27307, 1, 6]))
+        # Test consistency of data in .mgh and mri_convert produced .nii
+        nitest_path = os.path.join(get_nibabel_data(), 'nitest-freesurfer')
+        mgh = mghload(os.path.join(nitest_path, 'fsaverage', 'surf',
+                                   'lh.orig.avg.area.mgh'))
+        nii = load(os.path.join(nitest_path, 'derivative', 'fsaverage', 'surf',
+                                'lh.orig.avg.area.nii'))
+        assert_equal(mgh.shape, nii.shape)
+        assert_array_equal(mgh.get_data(), nii.get_data())
+        assert_array_equal(nii.header._structarr['dim'][1:4],
+                           np.array([27307, 1, 6]))
+        # Test writing produces consistent nii files
+        with InTemporaryDirectory():
+            nii.to_filename('test.nii')
+            nii2 = load('test.nii')
+            assert_equal(nii.shape, nii2.shape)
+            assert_array_equal(nii.get_data(), nii2.get_data())
+            assert_array_equal(nii.get_affine(), nii2.get_affine())
+
     def test_qform_sform(self):
         HC = self.header_class
         hdr = HC()

nibabel/tests/test_nifti1.py

@@ -34,7 +34,11 @@ class _Nifti2Mixin(object):
     sizeof_hdr = Nifti2Header.sizeof_hdr
     quat_dtype = np.float64
 
-    def test_freesurfer_hack(self):
+    def test_freesurfer_large_vector_hack(self):
+        # Disable this check
+        pass
+
+    def test_freesurfer_ico7_hack(self):
         # Disable this check
         pass