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FIX: Set CIFTI-2 dimensions in the last three entries of dim #930

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Merged
merged 3 commits into from
Jul 2, 2020
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FIX: Set CIFTI-2 dimensions in the last three entries of dim #930

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582cdfa
ENH: Update NIfTI header dimensions for CIFTI-2 compliance
mgxd Jul 2, 2020
f2f6dc9
RF: Set NIfTI-2 header shape through API call
effigies Jul 2, 2020
3667373
DOC: Add the spec text to explain the dim discrepancy
effigies Jul 2, 2020
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16 changes: 14 additions & 2 deletions nibabel/cifti2/cifti2.py
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Original file line number Diff line number Diff line change
Expand Up @@ -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()
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