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Questions tagged [medical-imaging]

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.

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Converting DICOM image to numpy array of shape (s, 3, 256, 256)

I've got folders with MRI images in them and I'm trying to replicate the MRnet study with my own data. Their model works on 1 .npy file per subject, shape (s, 3, 256, 256), with s being number of slices for a given subject (varies between…
user3078100
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fsl resampled image comes out cropped

I am using fsleyes to resample image by providing reference image, but the generated resampled image is cropped ? the blue is resampled overlay I tried increasing the resolution of reference image but that doesn't help either.
Sarah
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What types of animation does VTK support for poygonal meshes?

I've a bunch of expereince in 3D rendering from a game-dev perspective but very little with serious toolkits like VTK. We have a 3D model of a medical device which has a couple of degrees of motion, and we need to visualise this, animated, in a…
Mr. Boy
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OutOfRangeError: RandomShuffleQueue '_7_shuffle_batch_1/random_shuffle_queue' is closed and has insufficient elements (requested 200, current size 0)

really thank you to read my problem My dataset is about 9779 images(.dcm). There are two labels, One is 1, who has 5000 training images, and the other is 0, who has 4779 images. I use TFrecords to merge and build a dataset. Then feed it to a CNN…
Tozz
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What is an easy way to build CGAL mesh out of DICOM sequence?

I have a sequence of DICOM images constituting a single scan. I would like to build a CGAL mesh representing 3D volume segmented out of that scan by thresholding. I prefer Windows and few, easy to build dependencies, if any. I've heard that ITK can…
Paul Jurczak
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DICOM 3d display - Java 3D vs VTK

I'm going to work on implementing 3d display of dicom files and I'm wondering which technologies is easier to use: Java 3D or VTK? I'm not very experienced programmer,but I've already created a DICOM viewer based on dcm4che open source library. Any…
user2979961
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DICOM to grayscale in matlab

How can I convert a DICOM image into a grayscale image in matlab? Thanks.
Simplicity
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how to get an axial image from ct scan images. as i am using sliver07 dataset so it has 100+ images in single .mhd file

i using SLIVER07 dataset for liver segmentation task but i am stuck in reading that images. import SimpleITK as sitk import numpy as np import matplotlib.pyplot as plt # reading .mhd file from slive07 dataset itkimage =…
Qazi Sami Ullah Khan
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Center cropping of 3D images for MRI images

I have a list of 3D MRI images, and I would like to crop these images to the center so that I leave only the ROI, any suggestions on how to do that? I tried the following code, but it returned the original size at the end... Any idea how to crop all…
Mrmr
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Using Pseudo Color Softcopy Presentation State with Weasis dicom viewer

I plan to use Pseudo Color Softcopy presentation state(PCSPS) to map pixel values from grayscale space to rgb space. I don't want set the photometric interpretation in the original dicom file to 'Palette color'(it's MONOCHROME2) and add color lut to…
bharys
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Is there some methods with higher effiency to calculate the cordinates of cross section in a 3D array?

In my opinion, i will sovle it in two ways. The first one is to iterate all points in 3D array and judge if the points is in the plane constructed by given 3 points, the second one is to use region-growth and line-segment affine to do that. However,…
乔晓飞
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Writing int16 numpy array as an proper image

I am trying to write(save) a int16 numpy array as an image using openCV. Find the numpy file of an image in the link below: https://drive.google.com/file/d/1nEq_CeNmSgacARa2ADr_f_qVaSfJSZZX/view?usp=sharing The image I saved in bmp or png or tiff…
Senthil Kumar
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How to extract lungs part from the chest CT image in python or MATLAB

I have CT scan image and I want to extract (segment) only lungs part from that using python or MATLAB.
codewarrior
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How to generate 3D mesh from CT Slices (.raw) using marching cubes algorithm in C#?

I am trying to generate 3D mesh (isosurface extraction) from CT slices(.raw file) using the marching cubes algorithm. The RAW data is 8 bits 512x512 px and 207 slices. So the input is CT Raw data and the output is a 3D mesh of the CT Object Can you…
Dhaour9x
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How can I obtain axial slices of a 3D medical image saved as numpy array in python?

I have 3D volume medical image of size [284,143,143]. I want to extract axial slices from them and save them separatley in a folder. Can anyone tell me how can I acheive this in python.
CS.Enthu
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