GE data: 'DICOM File Meta Information header or the 'DICM' prefix missing from header

[RebeccaThornley]

Reporting this on behalf of David Price. When trying to run acr_snr on data from a GE scanner, he recieved the following error:
pydicom.errors.InvalidDicomError: File is missing DICOM File Meta Information header or the 'DICM' prefix is missing from the header. Use force=True to force reading.

Full code from terminal
(hazen-venv) davidprice@medphys037-mac ~ % hazen acr_snr ACR_Hd_tra_SNR1 --measured_slice_width=5.2 --subtract ACR_Hd_tra_SNR2 --report
2024-06-13 08:04:32 I [ACRObject.py:sort_dcms:47] image orientation is axial
2024-06-13 08:04:32 I [ACRObject.py:order_phantom_slices:78] Slice order inversion is not required.
Traceback (most recent call last):
File "/Users/davidprice/hazen-venv/bin/hazen", line 8, in
sys.exit(main())
File "/Users/davidprice/hazen-venv/lib/python3.9/site-packages/hazenlib/init.py", line 155, in main
result = task.run()
File "/Users/davidprice/hazen-venv/lib/python3.9/site-packages/hazenlib/tasks/acr_snr.py", line 88, in run
data2 = [pydicom.dcmread(dicom) for dicom in filepaths]
File "/Users/davidprice/hazen-venv/lib/python3.9/site-packages/hazenlib/tasks/acr_snr.py", line 88, in
data2 = [pydicom.dcmread(dicom) for dicom in filepaths]
File "/Users/davidprice/hazen-venv/lib/python3.9/site-packages/pydicom/filereader.py", line 1029, in dcmread
dataset = read_partial(
File "/Users/davidprice/hazen-venv/lib/python3.9/site-packages/pydicom/filereader.py", line 780, in read_partial
preamble = read_preamble(fileobj, force)
File "/Users/davidprice/hazen-venv/lib/python3.9/site-packages/pydicom/filereader.py", line 724, in read_preamble
raise InvalidDicomError(
pydicom.errors.InvalidDicomError: File is missing DICOM File Meta Information header or the 'DICM' prefix is missing from the header. Use force=True to force reading.
(hazen-venv) davidprice@medphys037-mac ~ % force=True
(hazen-venv) davidprice@medphys037-mac ~ % hazen acr_snr ACR_Hd_tra_SNR1 --measured_slice_width=5.2 --subtract ACR_Hd_tra_SNR2 --report

I will try and dig out images and send to Molly via email

[mollybuckley]

Hi Becky, thanks for flagging this - I think it works now! Adding the force=True statement as an argument in the dcmread function in acr_snr (line 88) forces the function to read the DICOM files even if the prefix is not as expected