Use this tag to ask question about processing/converting/creating/analyzing image instance in-memory/persistence-storage related to medical domain. This include DICOM images/pixel-data as well. Additional tag [tag:dicom] is only needed if question relates to DICOM Specifications. If question can stand without it, avoid using [tag:dicom] tag. This tag is agnostic to programming language or toolkit.
Questions tagged [medical-imaging]
250 questions
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accurate detection of circles in special medical images
I have many medical images with dcm file format. There are circles in the photos (6 circles but the sixth is too small to see).
I want to calculate the radius of these circles very precisely. At least the radius of the first three or two circles I…
shm
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VTK resliceCursorWidget compatibility with QT
I am working on the medical GUI development with QT and VTK. I have made MPR (MultiPlanar reformation) in VTK alone, but it does not display when I show it in QT (basically I add the renderwindow and renderer to QVTKWidget). I also tried…
Yinan Liu
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How to read multiple Nifti files from the same folder with Nibabel?
I did see a couple of tuts related to Nibabel, that work fine when you are reading only one nii image, but I need to read 167 files from the same folder, and I don't understand how to do it.
I tried using glob as we use it for OpenCV, but it doesn't…
John
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Is it possible to retrieve beam real world position from RT PLAN
I am currently working on some radiotherapy plan generation and I am trying to retrieve the beam source position from a DICOM RTPLAN file and point it on a related CT-Scan 3D image.
With the RTPLAN, I am able to access the isocenter position of each…
Argava
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Image note correctly displayed after transforming to Hounsfield Units
I am working on CT scans and specifically interested in the liver area. I am trying to convert pixel values to Hounsfield Units using the following function in python:
def transform_to_hu(slices):
images = np.stack([file.pixel_array for file in…
Dushi Fdz
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Orienting VTK PolyData objects in the same direction
I have different objects coming from DICOM files (isolated bones) loaded with vtk as meshes (vtkPolyData). Each one has a different orientation and I'm trying to rotate them at the appropriate angles so that all of them share the same maximum…
Luis
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Python - Convert pixel value to Hounsfield Units
I'm working on image chest scans, I am trying to convert pixel values on Hounsfield Units.
I'm using python for that purpose, my scans have different ranges and the problem is, window of (width of 3200, and center of 450)?
How can I make those scans…
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Conditional GAN (pix2pix) OR CycleGAN?
I have a dataset including paired MRI and CT of patients. My aim is generating synthetic CT from MRI images. As I have paired images, which GAN network is the best for this purpose? CycleGAN OR pix2pix? Which one result in a synthetic CT with a…
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Resize the Depth of CT data in Python
I have multiple CT datasets in Dicom format all with varying number of slices or 2D CT images.
Example:
Dataset 1 Shape: (512 x 512) x 100
Dataset 2 Shape: (512 x 512) x 130
Dataset 3 Shape: (512 x 512) x 122
How can I resize the data such that the…
user9209723
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Monai : RuntimeError: Sizes of tensors must match except in dimension 1. Expected size 7 but got size 8 for tensor number 1 in the list
I am using Monai for the 3D Multilabel segmentation task. My input image size is 512x496x49 and my label size is 512x496x49. An Image can have 3 labels in one image. With transform, I have converted the image in size 1x512x512x49 and Label in…
Ankita
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Why is there a difference in Intersection over Union (IoU) calculation while evaluating for same data using same model?
I evaluated the IoU score for the test dataset using the saved model.
(model.evaluate(test_gen, steps)
Also, I have calculated the IoU score for each image in the test dataset. When I calculate the average of the individual IoU values, the result…
Abu Noman Md Sakib
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how to extract a particular region of interest from an mri image(not manually) when same intensities of other unimportant are also present?
I want to extract the endotracheal region from the MRI of the Sagittal plane of the neck image, but after applying image processing techniques like thresholding, contour detection and binary masking,
I could find that there are other undesired…
smkd
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How to set voxel value based on absolute distances/coordinates from origin in simpleITK
I have a dicom 3D image and additional file describing binary mask. Binary mask is encoded with XYZ coordinates:
5.123422, 6.123123, 5.123123; 5.123422, 6.123123, 5.123123; 5.123422, 6.123123, 5.123123 ...
I want to transform those encoded points…
andyPity
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Filtered Back Projection : Cannot reconstruct image using backprojection Algorithm
I am learning FBP and for the last 1 month, I am stuck on Backprojection Algorithm. I have done the following steps till now.
Create Sinogram (Radon Transform)
Create Filter (hanning Filter: i used the hanning window function to implement the…
Rohit Das
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Combining two image label to one label
I have medical images for the prostate where each image has two anatomical labels label0= background label1= peripheral zone, Label2= transitional zone.
I would like to combine two labels so that they become one label and will form the whole…
Mrmr
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