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lab-midas / TCIA_processing

autoPET TCIA pipeline
MIT License
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OverflowError: Python integer -1024 out of bounds for uint16 #3

Open ivishalanand opened 1 week ago

ivishalanand commented 1 week ago

Getting this error

(tcia-processing) ➜  ThirdEyeVision python3 -W ignor
e /Users/vishalanand/Desktop/ThirdEyeVision/code/pet-ct-images/tcia_dicom_to_nifti.py /Users/vishalanand/Desktop/ThirdEyeVision/DATASET/TCIA-PETCT-DATA/manifest-1654187277763/FDG-PET-CT-Lesions /Users/vishalanand/Desktop/ThirdEyeVision/DATASET/TCIA-PETCT-DATA/manifest-1654187277763/FDG-PET-CT-Lesions-NIFTI/
  0%|                        | 0/36 [00:00<?, ?it/s]The following patient directory is being processed:  PETCT_0168f65af8
Traceback (most recent call last):
  File "/Users/vishalanand/Desktop/ThirdEyeVision/environments/tcia-processing/lib/python3.10/site-packages/dicom2nifti/convert_dir.py", line 85, in convert_directory
    convert_dicom.dicom_array_to_nifti(dicom_input, nifti_file, reorient)
  File "/Users/vishalanand/Desktop/ThirdEyeVision/environments/tcia-processing/lib/python3.10/site-packages/dicom2nifti/convert_dicom.py", line 118, in dicom_array_to_nifti
    results = convert_generic.dicom_to_nifti(dicom_list, output_file)
  File "/Users/vishalanand/Desktop/ThirdEyeVision/environments/tcia-processing/lib/python3.10/site-packages/dicom2nifti/convert_generic.py", line 274, in dicom_to_nifti
    data = common.get_volume_pixeldata(dicom_input)
  File "/Users/vishalanand/Desktop/ThirdEyeVision/environments/tcia-processing/lib/python3.10/site-packages/dicom2nifti/common.py", line 312, in get_volume_pixeldata
    slice_data = _get_slice_pixeldata(slice_copy)
  File "/Users/vishalanand/Desktop/ThirdEyeVision/environments/tcia-processing/lib/python3.10/site-packages/dicom2nifti/common.py", line 354, in _get_slice_pixeldata
    return apply_scaling(data, dicom_slice)
  File "/Users/vishalanand/Desktop/ThirdEyeVision/environments/tcia-processing/lib/python3.10/site-packages/dicom2nifti/common.py", line 508, in apply_scaling
    return do_scaling(data, rescale_slope, rescale_intercept)
  File "/Users/vishalanand/Desktop/ThirdEyeVision/environments/tcia-processing/lib/python3.10/site-packages/dicom2nifti/common.py", line 539, in do_scaling
    minimum_required = min([minimum_required, minimum_required * rescale_slope + rescale_intercept,
OverflowError: Python integer -1024 out of bounds for uint16
  0%|                        | 0/36 [00:00<?, ?it/s]
Traceback (most recent call last):
  File "/Users/vishalanand/Desktop/ThirdEyeVision/code/pet-ct-images/tcia_dicom_to_nifti.py", line 215, in <module>
    convert_tcia_to_nifti(study_dirs, nii_out_root)
  File "/Users/vishalanand/Desktop/ThirdEyeVision/code/pet-ct-images/tcia_dicom_to_nifti.py", line 199, in convert_tcia_to_nifti
    dcm2nii_CT(ct_dir, nii_out_path)
  File "/Users/vishalanand/Desktop/ThirdEyeVision/code/pet-ct-images/tcia_dicom_to_nifti.py", line 65, in dcm2nii_CT
nii = next(tmp.glob('*nii.gz'))
ivishalanand commented 1 week ago

I only downloaded a sample of data from the tcia ( 10 -12)