[Neuroimaging] Can it be used to make npy files from dcom?

[Matthew Brett]

Hi,

On Wed, Jul 22, 2020 at 9:58 AM Bjarni J <bjarnijo90 at gmail.com> wrote:
>
> Hi can nibabel be used to create npy files from a dicom image? I have a bunch of dicom's that I want converted to numpy arrays but I can't seem to find a good solution.
>

Can you just use the pydicom package for this?

[ins] In [1]: import pydicom

[ins] In [2]: dcm = pydicom.read_file('1.dcm')

[ins] In [3]: arr = dcm.pixel_array

[ins] In [4]: arr
Out[4]:
array([[   0,    1,    2, ...,  253,  254,  255],
       [ 256,  257,  258, ...,  509,  510,  511],
       [ 512,  513,  514, ...,  765,  766,  767],
       ...,
       [3328, 3329, 3330, ..., 3581, 3582, 3583],
       [3584, 3585, 3586, ..., 3837, 3838, 3839],
       [3840, 3841, 3842, ..., 4093, 4094, 4095]], dtype=uint16)

Cheers,

Matthew