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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Using the affine2d command with the dicom images in matlab
I wanted to move the DICOM images around x-axis with the value 4.2 milimeter and have written the following code:
srcFile2=dir('C:\Users\User\Desktop\Projekt\meine B.A\Programmieren\Archiv CBCT_A_04_08\*.dcm');
for i=1:88
…
Jack Georg
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How to handle image with extension .nii.gz? Is it possible to convert them in grayscale format like (240,240)?
I have always work with images with extensions .png, .jpg, .jpeg Now, I have seen medical images with extension .nii.gz
I'm using python and I have read it with the following code:
path = "./Task01_BrainTumour/imagesTr"
path_list =…
Azzurra
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How can I resize a mask and RGB image to match by cropping out unwanted regions in both images
I am working on a cell counting project with a histology dataset of RGB images and their corresponding masks. However, I have been stuck for over a week now on resizing the RGB and masks images to only the FOV by cropping out the regions of zero…
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`flow_from_dataframe()` custom pre-processing
I'm trying to use the keras ImageDataGenerator.flow_from_dataframe() method to generate image data on the fly as the dataset I'm working on is too large to load into memory in one go.
The source image data files are DICOM files, not supported by the…
moo
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Validation Accuracy of Siamese CNN not increasing, stucks at 0.50
I'm training a Siamese CNN model based on X-ray dataset and it gets stuck at 0.50 validation accuracy. Moreover, training and validation loss decrease while training accuracy hovers around 0.50 as well.
I think that is a error or something, but I…
leo-freecss
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How to store .npy file as a folder containing images
I am using the GRAD-CAM module that converts the images in a folder first to an array X and then after performing operations to a .npy file. But I would like to have this array back in image format and stored in a folder. How can I proceed…
AMANDEEP KAUR
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How to pass multiple files(.nii format) as input file using python command line?
I have a folder with 20 .nii files. Need to convert it into png, so using python nii2png.py for the same. nii2png.py This is the file I am making changes in. Here are 2 files for your reference: Here these are 2 .nii files.
It has the following…
AMANDEEP KAUR
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Conversion of .mhd format to .nii format for multiple files code runs without error, but no conversion done
I am using the sliver07 dataset and my task is to convert.mhd format images to .nii format.
Following the answer of Medical Imaging Data - how to convert .raw/mhd to Nifti/nii, I was able to convert it for 1 image but now as I apply it for multiple…
AMANDEEP KAUR
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InvalidArgumentError: Incompatible shapes: [8,3] vs. [8,4]
I'm doing an object detection and classification problem with DICOM images containing X-Rays scans of four classes. My model works when I convert all images into a numpy array and fit it to the model. But then I decided to write an image generator…
Bridge
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How to open .vol files (from 3D ultrasound) in python?
I work with so called cartesian .vol files that come from GE Voluson S6 ultrasound.
I'm able to open them in Slicer 3D application and display a 3-dimensional model as expected.
I'm aiming to convert these files to .stl in order to be able to use…
GraphitePearl
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Working with .tiff images in python for deep learning
I am currently working on a project using imaging flow cytometry images in python. the images are .tiff an example file name is image27_Ch1.ome.tiff . I am having a little trouble with opening these images. I have tried to use matplotlib and PIL and…
Zachary Anstey
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1 answer
Apply gaussian filter only on the edge
I have a binary mask, how to apply a Gaussian kernel of standard unit deviation on the border of the mask to smooth border?
Shawn Zhuang
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Combining different feature vectors for, SVM training for MRI classification
I've been currently working on my FYP on Brain tumor classification.Extracted features using wavelet transform ,glcm ,polynomial transform etc.
IS IT RIGHT TO APPEND THESE FEATURE VECTORS (columnwise) for training? like combinations of these…
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2D convolution along three orthogonals (axis) for 3D volumetric image
Since 3D convolution requires too much computational cost, so I prefer to use 2D conv. My motivation here is using 2D conv for volumetric images to reduce this cost.
I want to apply 2D convolution along three orthogonals to get 3 results, each…
vaveila
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Detect if there is camera motion in a video with moving objects in surgical video
I am trying to differentiate between camera motion and tool motion in a surgical video.
I have tried optical flow using opencv farneback and pass the results to an ML model to learn but no success.a major issue is getting good keypoints in case of…
Khushi
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