PyDICOM can't read pixel data and needs GDCM or Pillow

Question

I'm using pydicom and my code is pretty straightforward:

image = np.stack([s.pixel_array for s in scans])

But this gives a runtime error:

RuntimeError: The following handlers are available to decode the pixel data however they are missing required dependencies: GDCM (req. GDCM), Pillow (req. Pillow)

I'm not sure what to do. Any help would be.. helpful.

For any compressed pixel data, pydicom uses an external library to decompress the data. As indicated, you need to install either GDCM or Pillow to handle that particular file. — darcymason, Feb 13 '19 at 20:10
I’m having an impossible time installing it: https://stackoverflow.com/q/54676488/239879 — Shamoon, Feb 13 '19 at 21:22

score 6 · Accepted Answer · answered Feb 18 '19 at 08:25

6

If GDCM is giving you problems, give Pillow a go.
python -m pip install pillow
Make sure to install in the correct environment.

answered Feb 18 '19 at 08:25

g_uint

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score 3 · Answer 2 · answered Aug 04 '20 at 08:12

3

I have encountered the same problem and I already had pillow installed. The solution was to update pydicom and install gdcm (see here) as pointed out in this post by @Ali Türkay Avci. Using anaconda, you do:

conda install -c conda-forge gdcm

answered Aug 04 '20 at 08:12

My Work

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score 2 · Answer 3 · answered Dec 09 '21 at 02:28

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Installing python-gdcm solved my problem

pip install python-gdcm

answered Dec 09 '21 at 02:28

kdebugging

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PyDICOM can't read pixel data and needs GDCM or Pillow

3 Answers3

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