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
2
votes
1 answer
How to fit two images into one image
I am working on a project to fuse two DICOM Image by myself.
Image 1 (168x168)
When the images of Image 2 (512x512) are combined, the two images do not match at all.
I don't think there's a problem with the merging script, but
If you think the…
로다현
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2
votes
1 answer
U-Net segmentation without having mask
I am new to deep learning and Semantic segmentation.
I have a dataset of medical images (CT) in Dicom format, in which I need to segment tumours and organs involved from the images. I have labelled organs contoured by our physician which we call it…
jonedabb
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2
votes
2 answers
How to convert a 1D signal to 2D signal?
I have a 1 Dimensional signal (EEG signal) and I want to convert it to a 2D signal in order to use it as input for a CNN model. Can I use a Fourier transform to do that?
wassidi
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2
votes
1 answer
"AttributeError: 'numpy.ndarray' object has no attribute 'values'
Here's a snippet of my code:
#code sample
for i in range(1, number_of_segments + 1):
I1 = (dcm_pixel_array["array" + str(3 + (i - 1))]) * 2
I8 = (dcm_pixel_array["array" + str(3 + (7*int((number_of_segments+2)/8)) + (i-1) + 2)]) * 2
for…
NorthWind4721
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2
votes
0 answers
vtkImageAppend doesn't seem to be producing valid vtkImageData
I have a few DICOM stacks for different bones in a hand and I want to 3-D render the entire hand. So far I can only get a single bone to render.
I am using the python vtk and vtkplotter libraries.
So far I've tried creating a vtkImageData object…
anlrice
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2
votes
2 answers
Resample all images in the database to the same voxel size
I have 3 dicom stacks of size 512x512x133, 512x512x155 and 512x512x277. I would like to resample all the stack to make the sizes 512x512x277, 512x512x277 and 512x512x277. How to do that?
I know I can do resampling using slice thickness and pixel…
Avijit Dasgupta
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1
vote
1 answer
MATLAB: I am trying to create a GUI where I can scroll through a stack of 3-d images
I am working on a project in which I need to scrutinize individual images in a stack (CT scans). I do not like the montage function as the stack is 159 images thick. I am trying to create a gui that allows me to scroll through the individual images…
Younce-Davis
- 11
- 3
1
vote
2 answers
SimpleITK Filtering with sitk.ConnectedThresholdImageFilter() wrong output
I have tried many things to segment gray_matter, white_matter and cs_fluid images using sitk.ConnectedThresholdImageFilter(). unfortunately, I couldn't. Please, let me know what I am doing wrong.
Here is the example code:
data_dir = "
Burak
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1
vote
1 answer
Medical Imaging with python
I have an image in DICOM format, this image is composed of a set of RAW files (a specific case 122, which would be the number of slices that the image would have, depth in Z). The size of the image is 512x512x122 voxels.
The program I have made…
dms
- 11
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1
vote
2 answers
read nifti files 3d slicer vs other methods
I have some nii.gz files which, when I open using imajeJ , or any python library such as SimpleITK or Monai I get a stack of MRI images, as if taken from top to bottom. That being said, when I open the same file with slicer, I also get a stack of…
Iliasp
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1
vote
1 answer
Extract DICOMDIR slices and convert to mp4 file
I have a DICOMDIR file with a lot of dcm files in it. I have extracted the .dcm file with Instance Number 1. It has 49 slices/frames. I wnat to convert those frames into an mp4 format. My code gives and output but the video is still and has a yellow…
user2381342
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1
vote
2 answers
How to create a list of DICOM files and convert it to a single numpy array .npy?
I have a problem and don't know how to solve:
I'm learning how to analyze DICOM files with Python and, so,
I got a patient exam, on single patient and one single exam, which is 200 DICOM files all of the size 512x512 each archive representing a…
1
vote
1 answer
Why does convolution doesn't work with non-normalized images?
I'm trying to sharpen an image using Unsharp masking, but using this technique on a normal greyscale image with pixel values in [0,255] returns a garbled image, however, when I first normalize my image to be in the range of [0,1] I get the expected…
nothatcreative5
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1
vote
1 answer
looking for a loss function sensitive to edges for medical image quality enhuncement
For an image-to-image translation task in which I want to generate high-quality images from low-quality images ( MRI Images), I need a loss function to highlight the edges and generate images with sharper edges.
Do you have any recommendation for…
Amirhossein Sanaat
- 11
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1
vote
1 answer
How to train a semantic segmentation model with multiple masks?
I am working on a project about semantic segmentation in medical concepts where each image has multiple masks and each mask shows a different disease in the human eye, now I don't exactly know how to train my model with multiple masks. Should I…
fatemeh_p
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