How To Extract/view All Frames Of A Multi-frame Dicom File?

I know I can view a dicom file using following code: import dicom from dicom.contrib.pydicom_PIL import show_PIL f = 'CT-MONO2-8-abdo.dcm' ds = dicom.read_file(f, force=True) sho

Solution 1:

pydicom supports reading pixel data. Refer this documentation.

pydicom tends to be “lazy” in interpreting DICOM data. For example, by default it doesn’t do anything with pixel data except read in the raw bytes:

import dicom
ds=dicom.read_file("MR_small.dcm")
ds.PixelData
'\x89\x03\xfb\x03\xcb\x04\xeb\x04\xf9\x02\x94\x01\x7f ...
...

About pixel_array

A property of Dataset called pixel_array provides more useful pixel data for uncompressed images. The NumPy numerical package must be installed on your system to use this property, because pixel_array returns a NumPy array:

importdicomds=dicom.read_file("MR_small.dcm")ds.pixel_arrayarray([[905,1019,1227,...,302,304,328],
       [ 628,  770,  907, ...,  298,  331,  355],
       [ 498,  566,  706, ...,  280,  285,  320],...,
       [ 334,  400,  431, ..., 1094, 1068, 1083],
       [ 339,  377,  413, ..., 1318, 1346, 1336],
       [ 378,  374,  422, ..., 1369, 1129,  862]],dtype=int16)ds.pixel_array.shape(64,64)

Document also explains about viewing images at http://pydicom.readthedocs.io/en/stable/viewing_images.html.

As explained in error message (and by @kritzel_sw in comment) the pydicom does not support the Transfer Syntax of source image yet. Change the Transfer Syntax using some other tool before attempting to extract the frames.

Another helpful blog of Rony http://dicomiseasy.blogspot.in/2012/08/chapter-12-pixel-data.html

Also check this Stack Overflow question; it is about old version but may be helpful.