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 correlate different MRI sequences images in NIFTI format?
I am new on Medical Imaging. I am dealing with MRI images, namely T2 and DWI.
I uploaded both images with nib.load, yet each sequence image has a different number of slices (volume, depth?). If I select one slice (z coordinate), how can get the…
Paul
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How I can change this operation imshow(im16,[WC-WW/2,WC+WW/2]); into a variable in matlab?
I want to save the operation imshow(im16, [WC-WW/2,WC+WW/2]); in a new variable. It is an image that I'm displaying a certain range, but I don't want to use imshow(), I only want to save a new image with a certain range of intensity window result of…
Eli Flowers
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How to set spacing in Frangi filter for 3D stack of DICOM data
I am using the Frangi filter for hepatic vessel segmentation.
The problem is that that data are not isotropic [1,1,1].
I can do resampling. It creates more slices but it looses pixels and its not so precise.
I found, that maybe I can change it…
user12651635
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how to project a polynomial-shape part of an image to a line?
I have a series of 2D images which i have fitted a 6th degree polynomial into:
I want to transform every 2D image into a line with respect to the polynomial and stack the lines so i get a 2D image (basically the job is to transform 3D CBCT-scan to…
Pariya Mehrbod
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How to get affine information from a DICOM file in python?
I have a folder with DICOM files inside (CT scan for example) and I need to extract affine information of the volume since I will produce a mask and need it later to align the volume and mask.
However the solution I have now is not optimal at all. I…
Joris Fournel
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1 answer
2D CNN to classify 3D Greyscale MRI data, possible data labeling issue
I am trying to run a binary classification of 3D black and white MRI data. I'm using 2D convolutions due to the lack of channels inherent in B&W data. I've added a dimension to get the dimensionality to line up, and essentially the depth of this…
John Newberry
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3D visualization of .dicom files with ipyvolume
i'm trying to visualize a set of .dicom files using pydicom and ipyvolume.
I used pydicom to read files and then sorted them by their location and turned the slices into a 3D array. I could draw a 3D model of the data using…
Pariya Mehrbod
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SegNet Implementation
I am working on Biomedical Image Segmentation. For this regard, i need the implementation of SegNet model. I searched for SegNet implementation in many places but none of these provide me correct implementation. I got some implementations without…
rifat ahommed
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RuntimeWarning: invalid value encountered in ushort_scalars
I am trying to make a T2 map from my dicom files, but am encountering the following errors with my code:
RuntimeWarning: invalid value encountered in ushort_scalars
T2 map: if math.log((I8[j][k]) / (I1[j][k])) == 0:
ExampleName.py:91:…
NorthWind4721
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How to decode and visualize DICOM curve data in Python 3?
I am trying to visualize a DICOM file with Python 3 and pyDicom which should contain a black 100x100 image with some curves drawn in it. The pixel data is extracted from header (7fe0,0010) and when printed shows b'\x00\x00\x00...'. This I can easily…
SMey1908
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How to convert Multiple png or Jpeg images into one nifti image by python3?
I have 191 different png images.
How can I convert them into one 3d nifti image?
Neamul
- 31
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1 answer
How to feed nifti Images in Conv Neural Network (Unet)
For my thesis I have 16 nifti MRI images (Dim: 162×162×192), My plan is to work with Conv Neural Network and I divided 10 and 6 images as train and test images.
The problem is, How to feed nifti images in Unet as train image for input and output as…
Neamul
- 31
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1 answer
Get data from remote Orthanc Server to Ohif viewer
I have my app which is working on docker.
On local version of app I run my Ohif viewer I am using command yarn run dev:orthanc.
Due to the fact that I want to have data from remote Orhtanc server I changed on package.json file script "dev:orthanc"…
Test123123
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3 answers
Convert CT Slices to Planar X-Ray Image
I have axial slices of chest CT scans. Now, I want to use all these slices to construct a planar structure like an X-ray with a coronal view (Posterior to Anterior or Anterior to Posterior view).
I have no idea how to proceed with this problem. One…
ChocoLite
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1 answer
How can I keep the association between image and coordinate (z-axis) after a preprocess function?
I'm working on a preprocessing function that takes DICOM files a input and returns a 3D np.array (image stack). The problem is that I need to keep the association between ImagePositionPatient[2] and the relative position of the processed images in…
Agostino Dorano
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