@vincent1bt Thanks for sharing your code tutorial.

I work with nii ct files.

With your code, I have been able to convert into hu and window the nii files fine.

But the mask, pad and crop just doesn't work. Any reason for this?

Masking output on regular and HU file

Cropping output on regular and HU file

Padding output on regular and HU file

I supply a single axial nii array slice to the functions for comparion and they don't work. Please help!

Followed the steps explained in notebook

I would like to know whay my resampled_image space showing (302, 302, 0). I believe that migh t be reason it's not displaying in plt.imshow

resampled_image = resample(first_image, image_thickness, pixel_spacing)

array([], shape=(302, 302, 0), dtype=uint16)

np.squeeze(resampled_image).shape
(302, 302, 0)

plt.imshow(resampled_image)

TypeError Traceback (most recent call last)
in
----> 1 plt.imshow(resampled_image)

~/anaconda3/lib/python3.7/site-packages/matplotlib/pyplot.py in imshow(X, cmap, norm, aspect, interpolation, alpha, vmin, vmax, origin, extent, shape, filternorm, filterrad, imlim, resample, url, data, **kwargs)
2681 filternorm=filternorm, filterrad=filterrad, imlim=imlim,
2682 resample=resample, url=url, **({"data": data} if data is not
-> 2683 None else {}), **kwargs)
2684 sci(__ret)
2685 return __ret

~/anaconda3/lib/python3.7/site-packages/matplotlib/init.py in inner(ax, data, *args, **kwargs)
1599 def inner(ax, *args, data=None, **kwargs):
1600 if data is None:
-> 1601 return func(ax, *map(sanitize_sequence, args), **kwargs)
1602
1603 bound = new_sig.bind(ax, *args, **kwargs)

~/anaconda3/lib/python3.7/site-packages/matplotlib/cbook/deprecation.py in wrapper(*args, **kwargs)
367 f"%(removal)s. If any parameter follows {name!r}, they "
368 f"should be pass as keyword, not positionally.")
--> 369 return func(*args, **kwargs)
370
371 return wrapper

~/anaconda3/lib/python3.7/site-packages/matplotlib/cbook/deprecation.py in wrapper(*args, **kwargs)
367 f"%(removal)s. If any parameter follows {name!r}, they "
368 f"should be pass as keyword, not positionally.")
--> 369 return func(*args, **kwargs)
370
371 return wrapper

~/anaconda3/lib/python3.7/site-packages/matplotlib/axes/_axes.py in imshow(self, X, cmap, norm, aspect, interpolation, alpha, vmin, vmax, origin, extent, shape, filternorm, filterrad, imlim, resample, url, **kwargs)
5669 resample=resample, **kwargs)
5670
-> 5671 im.set_data(X)
5672 im.set_alpha(alpha)
5673 if im.get_clip_path() is None:

~/anaconda3/lib/python3.7/site-packages/matplotlib/image.py in set_data(self, A)
688 or self._A.ndim == 3 and self._A.shape[-1] in [3, 4]):
689 raise TypeError("Invalid shape {} for image data"
--> 690 .format(self._A.shape))
691
692 if self._A.ndim == 3:

TypeError: Invalid shape (302, 302, 0) for image data

Hi, how to obtain the window width and window center values from a nifti image?

Hi Vincent,

Could you share the sample data of AD.ipynb?

ad-2d.zip
cn-2d.zip

It would be nice to run it on Collab.

Thanks and happy holidays