Source code for my blog post tutorial about how to use deep learning on MR images.
Home Page: https://sites.duke.edu/mazurowski/2022/07/13/breast-mri-cancer-detect-tutorial-part1/
License: MIT License
Hey,
I'm trying to implement your amazing tutorial but keeps giving me this error.
FileNotFoundError: [Errno 2] No such file or directory: 'D:/manifest-1654812109500/Duke-Breast-Cancer-MRI/Breast_MRI_001/1.3.6.1.4.1.14519.5.2.1.186051521067863971269584893740842397538/1.3.6.1.4.1.14519.5.2.1.185777849803665244536713316058283493877/1-01.dcm'
this is my paths definition:
data_path = 'D:/manifest-1654812109500'
boxes_path = 'D:/Annotation_Boxes.csv'
mapping_path = 'D:/Breast-Cancer-MRI-filepath_filename-mapping.csv'
target_png_dir = 'png_out'
if not os.path.exists(target_png_dir):
#os.makedirs(target_png_dir)
the completed message:
FileNotFoundError Traceback (most recent call last)
~\AppData\Local\Temp\7\ipykernel_8036\3333985462.py in save_dcm_slice(dcm_fname, label, vol_idx)
14 try:
---> 15 dcm = pydicom.dcmread(dcm_fname)
16 except FileNotFoundError:
C:\ProgramData\Anaconda3\lib\site-packages\pydicom\filereader.py in dcmread(fp, defer_size, stop_before_pixels, force, specific_tags)
992 logger.debug("Reading file '{0}'".format(fp))
--> 993 fp = open(fp, 'rb')
994 elif fp is None or not hasattr(fp, "read") or not hasattr(fp, "seek"):
FileNotFoundError: [Errno 2] No such file or directory: 'D:/manifest-1654812109500\\Duke-Breast-Cancer-MRI/Breast_MRI_001/1.3.6.1.4.1.14519.5.2.1.186051521067863971269584893740842397538/1.3.6.1.4.1.14519.5.2.1.185777849803665244536713316058283493877/1-001.dcm'
During handling of the above exception, another exception occurred:
FileNotFoundError Traceback (most recent call last)
~\AppData\Local\Temp\7\ipykernel_8036\536749713.py in <module>
39 if ct_negative >= N_class:
40 continue
---> 41 save_dcm_slice(dcm_fname, 0, vol_idx)
42 ct_negative += 1
~\AppData\Local\Temp\7\ipykernel_8036\3333985462.py in save_dcm_slice(dcm_fname, label, vol_idx)
25 dcm_fname_split[-1] = dcm_fname_end
26 dcm_fname = '/'.join(dcm_fname_split)
---> 27 dcm = pydicom.dcmread(dcm_fname)
28
29
C:\ProgramData\Anaconda3\lib\site-packages\pydicom\filereader.py in dcmread(fp, defer_size, stop_before_pixels, force, specific_tags)
991 caller_owns_file = False
992 logger.debug("Reading file '{0}'".format(fp))
--> 993 fp = open(fp, 'rb')
994 elif fp is None or not hasattr(fp, "read") or not hasattr(fp, "seek"):
995 raise TypeError("dcmread: Expected a file path or a file-like, "
FileNotFoundError: [Errno 2] No such file or directory: 'D:/manifest-1654812109500\\Duke-Breast-Cancer-MRI/Breast_MRI_001/1.3.6.1.4.1.14519.5.2.1.186051521067863971269584893740842397538/1.3.6.1.4.1.14519.5.2.1.185777849803665244536713316058283493877/1-01.dcm'
The error is occurring because the Dicom files are stored with other paths, not the default you set in your code
1-001.dcm
for example:
D:\manifest-1654812109500\Duke-Breast-Cancer-MRI\Breast_MRI_001\01-01-1990-NA-MRI BREAST BILATERAL WWO-97538\8.000000-ax dyn 2nd pass-92755
Is there an easy way please to deal with this path issue ?
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