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 overlap two label to make mask for segmentation in ITK-snap?
I'm annotating CT scan slices(Nifti format) with ITK-snap. One slice contains two labels(Subarachnoid and Intraparenchymal) in the same area. Here is the original annotated image link: https://ibb.co/FJpyVZF
Since two labels are overlapping, the…
Ornob Rahman
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Extract pixels within quarter circle in python
I have an image which I want to extract the pixels of the specific part of that. This part is a quarter circle, and my desire is to obtain the pixels of that.
I have the coordinates of the center and points which the lines connected to the circle.…
Majid R
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Problem with assigning 2d array as a one slice of 3d array
I try to load series of DICOM files into 3d array. I do this on bad way because I got an error something like this (not fluent in Python):
ValueError: could not broadcast input array from shape (512,512) into shape (512,117).
I don't understand why,…
SunriseAvenue
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How to apply a palette to a bitmap
I am making a dicom viewer by myself.
Changing the color of the dicom image was successful, but it's a solid color.
So, to solve the monochromatic part, I brought the dicom palette.…
로다현
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Mapping values from NP ARRAY to STL
Recently i was struggling trying to take the pixel values of a 3D volume (np array) using specific space coordinate of a STL object.
The STL object is spatially overlapped with the 3D volume but the latter has no coordinate and so i don't know how…
Zimmer
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how to fusion two 16 bit images
I am working on a DICOM viewer project that combines PET and CT.
Progress
Adjust the size of one of the two dicom files to the larger one.
And change the color of one dicom file
And merge the two dicom files
example dicom bitmap1
bitmap2 ,…
로다현
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signaltonoise ratio use in medical imaging processing
greetings
today I saw on a post on StackOverflow this function for calculating SNR or signal to noise ratio from an input image.
the function code :
def signaltonoise(a, axis=0, ddof=0):
a = np.asanyarray(a)
m = a.mean(axis)
sd = a.std(axis=axis,…
Rico domeri
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- 3
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Load 3D image dataset
I am facing some problems to write the getitem() function in my dataset class. I am working on a MRI dataset (3D). Each file consists of 160 slices in DICOM format. I have transformed the DICOM files into PNG.
The structure of the files looks like…
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How to find connected components of a 3D CT scan Image using python?
I have some 3D CT scan images. Some slices of that image contains unnecessary things. I want remove that things giving the intensity value -1000. How can I do that?
a_variable
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How to volume render 3D numpy array using VTK (MarchingCubes) in Python?
I have a 3D numpy array and I am trying to volume render it using VTK. However, I get a completely different volume rendering when I visualise it. I suspect it has something to do with my conversion of numpy array to the VTK image format but I can't…
user42
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Unable to save iverseftt image and image K-Space in matlab
I have a brain MRi image in .png format. I read the image and extract the K-Space and set some of the K-Space as 0
img_fft = fftshift(fft2(img));
sizes = size(img_fft);
row_half = sizes(1)/2;
flag = true;
for r = row_half:sizes(1)
for c =…
Razor
- 89
- 9
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2 answers
What is the meaning of liver slice in CT Scan of Liver ? (Slice)
I did not understand the slice meaning in liver CT Scan images.
can you explain it? Like in the below code.
for file in tqdm(os.listdir(para.test_seg_path)):
seg = sitk.ReadImage(os.path.join(para.test_seg_path, file))
seg_array =…
Hazrat Bilal
- 11
- 1
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0 answers
A more efficient way of storing a large number of RGB images in an HDF5 file
I have a few hundred large images (more than 100K x 200K pixels). I am dividing each of these images into 256 x 256 patches and storing them all in a HDF5 file with the following structure:
Here is my code to recreate this HDF5 structure:
def…
avi.ks
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Why do I run out of memory on Spyder IDE?
I am working on image classification. I am working remotely, the work station has a memory of about 65GB. I am training about 100, 3d medical images using transfer learning. However, the memory on spyder IDE shows gradual increase until the code…
Kenan Morani
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How do I resample SimpleITK images to same direction (i.e. view)?
I would like to know how can I resample, for example 3D MRI Brain scans, from Coronal to Axial image view, without changing target image dimensions.
Image 1 information:
View: Coronal
Dimension: (256, 256, 128)
Image 2 information:
View:…
CodingAddict
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