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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adding an overlay on a DICOM image using open CV
I am trying to create a layer on a DICOM image, below code works fine for jpg/png images but not for DICOM.
import cv2
import numpy as np
import pydicom as dicom
ds=dicom.dcmread('D0009.dcm')
img=ds.pixel_array
blank =…
Saumya mishra
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How to use GDCM to write voxel data, slice by slice?
In all the examples I've seen for GDCM on how to write image data, they always consider the image volume as a single whole, cohesive buffer. The basic structure is along the lines
#include "gdcmImage.h"
#include "gdcmImageWriter.h"
#include…
datenwolf
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2 answers
How do I convert STL file to numpy array and format it to overlay with Dicom data?
I have STL files of 3D objects and I have converted them into both mesh objects and numpy arrays using the numpy-stl package. I have also converted DCM data into numpy arrays with the pydicom package, but the numpy array versions of the STL files…
Alex Richardson
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2 answers
How to create julia color scheme for displaying Ct scan Makie.jl
I use makie.jl with slicesNumb for visualization of PET/CT scans, I have 3d array of attenuation values and I display heatmap with changing slices using slider - this works well I have two problems
I do not know how to be able to define custom…
Jakub Mitura
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1 answer
Convert unet answer back to .nii file
I am new to deep learning, currently working on an image segmentation network. I managed to train the network, but the problem is to translate the network response into nii format. I cut the training sample from the CT images into 512X512 slices,…
Yossarian
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1 answer
Nearest neighbor interpolation in GLSL
I have a GLSL fragment shader as part of a pipeline that renders slices of two 3D volumes blended together. For one of the volumes, I would like to use nearest neighbor interpolation since it is a "segmentation mask" (i.e. at each voxel indicates,…
iv1
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Convert patient coordinates into voxel coordinates for DICOM images
I have a question pertaining to the conversion of patient coordinates into voxel coordinates of a 3D MRI point cloud model obtained from DICOM. I have a 3D point cloud file obtained from 2D MRI images, and the points are in the patient coordinate…
Ashritha Eadara
- 11
- 2
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0 answers
Recommended framework for medical application
I am in the startup process for writing a larger application for medical visualization and interaction. I am considering which pipeline to choose.
MITK: Uses ITK at its core. Algorithms inherit from itk::Process and object inherit from itk::Object…
Jens Munk
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How to make a local variables global in python
The model runs fine but I want to plot the results and cant seem to get it working, any help? I believe I have to make the local variable global for accuracy, loss, val_accuracy, val_loss but Im not sure how to do this in this case. I really need…
user15470345
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Average Pooling layer in Deep Learning and gradient artifacts
I know that in Convolution layers the kernel size needs to be a multiplication of stride or else it will produce artefacts in gradient calculations like the checkerboard problem.
Now does it also work like that in Pooling layers? I read somewhere…
Jarartur
- 149
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Image threshold algorithms to use on an x-ray image and detect bones
I have a little project with OpenCV (python) where one of my steps is to take an x-ray image from the human body and convert it to a binary image where white pixels represent where some bone is present and black means there is no bone there.
Since…
OverShifted
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Represent a 3D volume image from 2D images in Matlab
I should represent a 3D volume image from 2D images in Matlab. The number of 2D images is 90 images in DICOM format.
Besides, the each picture size is 512 * 512. This task is about the distance between slices in the Z-axis.
This is my following…
Natali Graß
- 25
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4 answers
Converting YBR_RCT Photometric Interpretation to RGB
I have a J2k Lossless dicom image and upon reading it with pydicom I see that it's in the YBR_RCT Color Space.
I want to convert the Color Space to RGB. I tried using the convert_color_space method from pydicom however, apparently this conversion is…
Gaurav Fotedar
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Neuroimage MRI scan CNN model preparation
I would like to know a couple of things to clear my confusion. I want to work on a medical neuroimage MRI image scans dataset from the ADNI database.
Each Alzheimer's Disease (AD) MRI image scan has multiple slices.
Do I have to separate each image…
Mjachowdhury
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How to maintain Direction in SimpleITK image to numpy array conversion?
I have three different isotropic MRI DICOM volumes of the same object, each with a different direction (orthogonal sagittal, coronal and transverse acquisitions of same object).
I would like to convert them to numpy arrays and plot them, in such a…
walew
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