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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How to transform Ultrasound images for simulation of CT images?
so I'd like to simulate CT images from ultrasound images using GAN and I am currently working on the data preparation.
By nature of the ultrasound these images are stored in a cone shaped kind of form:
But what I want to have is the image in the…
Destyl
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SimpleITK - Coronal/sagittal views problems with size
I'm trying to extract the all three views (Axial, Sagittal and Coronal) from a CTA in DICOM format, using the SimpleItk library.
I can correctly read the series from a given directory:
...
import SimpleITK as sitk
...
reader =…
Ghesio
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Training a Unet network for brainsegmentation
I have two questions:
Q1:
I was wondering what is the best way to feed the untet network with training data:
Sending in one patient at the time, where each volume is 160x3x192x192
Sending in random slices from k patients
Q2:
At the moment I have…
aram
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vtkplotter - How to set a colormap
I'm working with labeled DICOMs, and I'm using vtkplotter to visualize the 3D model. Each voxel has a label that identifies the recognized part of bone, ranging from -1024 to a value that varies according to the DICOM scan. How can I assign a…
Gibser
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TypeError: forward() missing 1 required positional argument: 'x' while implementing Grad CAM
I made model that takes grayscale image as input, and returns single value as output.
Backbone of this model is basically resnet18, but as it takes different input/output, I modified it.
model = models.resnet18(pretrained=True)
model.conv1 =…
brian lee
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How do I display all 8-bits image on python
first of all, sorry for my bad english, im a spanish speaker so Im gonna try my best to explain my problem.
I have a normalized ([0-255]) dicom image, and I want to display 8 images, but changing the bit depth, I mean like: 1bit image, 2bit image,…
Nicolas
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Manual registration with SimpleElastix
I'm using SimpleElastix (https://simpleelastix.github.io/) for the registration (Affine) of the two 2D images (see attached) . For this I'm using this code :
import SimpleITK as sitk
elastixImageFilter =…
jeanluc
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In python numpy array, how to know which object is nearer to one point in one image?
I have a numpy array, which respresents an image. The image has 3 colors: orange (background), blue (object1) and green (object2). I use 3 values (0, 1 and 2) to indicate the 3 colors in numpy array. Two objects are not overlapped.
My question is:…
Jingnan Jia
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How can I track different streamlines in DIPY?
I'm working on a project where i have to use DIPY to track different streamlines of the brain and show them separately, I found the code to track the Corpus Callosum on DIPY's official website. Only I couldn't understand how to make it track other…
Ridouane Hadj Aissa
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Difference in the output seen in radiant viewer after saving/writing same dicom image using sitk.Write
I'm reading a dicom image and accessing its pixel array. After that saving that array again into dicom format using sitk.Write but there is different between original image that is going to be read and same image after being written. How can I get…
Hachughtai97
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How to preprocess image data without too much consuming RAM?
This might seem a basic question, but I am stuck on it and would like to get some help.
I am trying to load and preprocess some images in DICOM Format in order to feed them to my Keras model, since I have about 2 thousand of images, RAM got consumed…
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Building 3D CNN for binary classification of greyscale MRI data, Data dimensionality issue when attempting model.fit
I'm trying to build a 3D CNN for binary classification of greyscale MRI data. I'm new to this, so don't pull any punches, I'm here to learn! I have a subsample of 20 3D files, with dimensions (189, 233, 197). I add a a dimension to act as the…
John Newberry
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Voxel normalization of third dimension in python
I´m currently working on normalizing ct-scans (x, y, layer). Normalizing the first two dimensions is simple using cv2.reshape, but the third dimension... My idea is to flatten the first two dimensions to get a 2d-numpy-array. If I do the reshape to…
Dennis182
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DICOM to Nifti metadata not transfering
I am trying to take a number of DICOM stacks and convert them to Nifti files. When I do the conversion and open the new Nifti file in a 3D viewer the volume is smashed together in the z direction. The Nifti files do not know what the spacing is…
rzaratx
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Trying to convert Dicom image files into png
Hi I have a folder of dcm files i want to change into png files to put into a png folder. Here is the code I have done:
dcm_folder= '/Users/riaroque/Desktop/DCM Pneumonia cases'
PNG_folder= '/Users/riaroque/Desktop/PNG…
Ria Roque
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