PyDICOM Returns KeyError Even Though Field Exists Question: I’m reading in a DICOM with pydicom.read_file() like this: x = pydicom.read_file(/path/to/dicom/) This returns an instance of FileDataset but I get an error when trying to access a value like this: x[0x20,0x32] OUTPUT: *** KeyError: (0020, 0032) I also tried accessing the value like this: x.ImagePositionPatient OUTPUT: …
Converting hand radiograph DICOM to PNG returns white/bright image Question: I am converting hand X-rays in DICOM format to PNG format. The code below does this: import os import cv2 import pydicom import numpy as np from PIL import Image inputdir = "P:/BoneDataset/DICOM-File/0-RefinedDICOM/" outdir = ‘P:/BoneDataset/DICOM-File/1-ConvertedPics/’ test_list = [f for f in os.listdir(inputdir)] for f …
Error when converting DICOM image to pixel_array using tensorflow_io Question: I am trying to create a TensorFlow Dataset from DICOM images using the tf.data API and tensorflow_io, and I want to perform some pre-processing using Hounsfield units from the images. The DICOM images have a shape of (512,512). I have extracted the PixelData from the …
Trying to input a RGB fMRI DICOM image, modify it, and save it as a grayscale dicom image in Python using pydicom Question: I am trying to take in an RGB fMRI scan as input and output the same scan but in grayscale with the color parts "burned" white essentially. Whenever I try and modify …
DICOM slicing orders in python Question: I have a question about slices ordering: I have about 80 pictures of hip joint but there are not arranged from feet to head or head to feet. Is there any way to arrange them in an intended order? # pixel aspects, assuming all slices are the same ps …
Using dicom Images with OpenCV in Python Question: I am trying to use a dicom image and manipulate it using OpenCV in a Python environment. So far I have used the pydicom library to read the dicom(.dcm) image data and using the pixel array attribute to display the picture using OpenCV imshow method. But the …
How to Install a Package in PyCharm when project interpreter is set to conda, and the package is not provided/listed by conda? Question: I installed pycharm on my computer. I set the project interpreter to acaconda3/bin/python because that is the python3 interpreter I used on my computer before installing pycharm. I was able to install …
Reading .dcm files from a nested directory Question: This is the form of my nested directory: /data/patient_level/study_level/series_level/ For each patient_level folder, I need to read the “.dcm” files from the corresponding “series_level” folder. How can I access the “.dcm” file in the “series_level” folders? I need 3 features from a DICOM object. This is my …
How to replace pixel data in same DICOM file using pyDicom to read it again with any DICOM viewer? Question: I want to read some DICOM files, so I’m testing pydicom for my work, which I think is considerably useful. Now I want to load existing DICOM files, replace the pixel data array with another …
