[Neuroimaging] Question about nibabel.processing

[Christopher Cox]

Hello,

My first question should really be: how do you review the archive for this mailing list? I imagine this question has been answered, but I do not know where to look.

I am attempting something very simple: I want to resample a volume. The nifti file on disk is 4D, and contains two volumes. Nibabel.processing.resample_to_output() will not work with 4D data. Fortunately for me, I only care about the first volume in this dataset. So I should have no problem.

But... nothing I can think to try works. I apologize it is difficult to read, but I've condensed several of my attempts into an interactive python session, and copied all of my work and the errors I am getting as a post script. I tried to color code, but that might not come through.

My first attempt is to try and pass the sliced data object (as in, data = img.get_data()), but that is a memory map as lacks the metadata the function requires. I tried passing the image (as in, img = nib.load(...)), but it cannot be sliced like the data can. I then tried simply loading only a single volume into memory (as in, vol0 = img.datobj[...,0]), but that doesn't work either (vol0 is a numpy array, and img is still seen as 4D).  I tried updating the shape metadata in img, but that's read only.

Thank you very much for helping me figure out the intended way to use this function.

Best,
Chris

Python 3.6.0 (v3.6.0:41df79263a11, Dec 23 2016, 08:06:12) [MSC v.1900 64 bit (AMD64)] on win32
Type "help", "copyright", "credits" or "license" for more information.
>>> import nibabel as nib
>>> nib.__version__
'2.1.0'

>>> import nibabel.processing
>>> img = nib.load('Template_6.nii')
>>> img.shape
(121, 145, 121, 2)

>>> data = img.get_data()
>>> r = nib.processing.resample_to_output(data[...,0], [3,3,3])
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "C:\Users\mbmhscc4\AppData\Roaming\Python\Python36\site-packages\nibabel\processing.py", line 242, in resample_to_output
    out_vox_map = vox2out_vox((in_img.shape, in_img.affine), voxel_sizes)
AttributeError: 'memmap' object has no attribute 'affine'

>>> r = nib.processing.resample_to_output(img, [3,3,3])
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "C:\Users\mbmhscc4\AppData\Roaming\Python\Python36\site-packages\nibabel\processing.py", line 242, in resample_to_output
    out_vox_map = vox2out_vox((in_img.shape, in_img.affine), voxel_sizes)
  File "C:\Users\mbmhscc4\AppData\Roaming\Python\Python36\site-packages\nibabel\spaces.py", line 76, in vox2out_vox
    raise ValueError('This function can only deal with 3D images')
ValueError: This function can only deal with 3D images

>>> r = nib.processing.resample_to_output(img[...,0], [3,3,3])
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
TypeError: __getitem__() takes 1 positional argument but 2 were given

>>> vol0 = img.dataobj[...,0]
>>> r = nib.processing.resample_to_output(vol0, [3,3,3])
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "C:\Users\mbmhscc4\AppData\Roaming\Python\Python36\site-packages\nibabel\processing.py", line 242, in resample_to_output
    out_vox_map = vox2out_vox((in_img.shape, in_img.affine), voxel_sizes)
AttributeError: 'numpy.ndarray' object has no attribute 'affine'

# This is after the previous attempt, loading only the first volume. img remains 4D
>>> r = nib.processing.resample_to_output(img, [3,3,3])
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "C:\Users\mbmhscc4\AppData\Roaming\Python\Python36\site-packages\nibabel\processing.py", line 242, in resample_to_output
    out_vox_map = vox2out_vox((in_img.shape, in_img.affine), voxel_sizes)
  File "C:\Users\mbmhscc4\AppData\Roaming\Python\Python36\site-packages\nibabel\spaces.py", line 76, in vox2out_vox
    raise ValueError('This function can only deal with 3D images')
ValueError: This function can only deal with 3D images


>>> img.shape = img.shape[0:3]
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
AttributeError: can't set attribute


Christopher R. Cox, PhD
Neuroscience and Aphasia Research Unit (NARU)
University of Manchester, UK
christopher.cox-2 at manchester.ac.uk<mailto:christopher.cox-2 at manchester.ac.uk>

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