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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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How do I convert a 4D image to a DICOM image in pydicom?

I have a 4D dicom image which I read with dcmread. Consequently, I change a few pixels to black in order to remove the imprinted patient information. However, if I want so save these changes I get errors. Code: pathFile='...' #Fill in…
Carlijn
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Error when converting DICOM image to pixel_array using tensorflow_io

I am trying to create a TensorFlow Dataset from DICOM images using the tf.data API and tensorflow_io, and I want to perform some pre-processing using Hounsfield units from the images. The DICOM images have a shape of (512,512). I have extracted the…
Kumaresh Balaji
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Direct Volume Rendering in Java - how does an RGB transfer function work?

I am creating a direct volume rendering application with the goal of writing at least 2 2d transfer functions and a 3d transfer function for determining colour and opacity values for voxels. I have a CT dataset - cthead[k][j][i] that will give me a…
codeine_cola
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How to feed Nifti Images in 3d CNN for classification?

I have 142 Nifti CT images of the brain, I converted them from Dicom. Every NIfti file has the dimension of 512×512×40. My plan is to work with 3d Conv Neural Network for multi-class classification. How should I feed Nifti images in a 3d CNN?
Ornob Rahman
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How to open folder, resize present images and save them in the same folder. (python)

For a project that I am working on I have to resize a lot of nrrd's. These files are stored in a very specific order and should also be returned to the same file. For the last few days I have been trying different ways to open the image, resize it…
Lars VanderBroeck
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Dicom deformable image registration

I have dicom files for two CT scans and deformable registration between them. I would like to ask how I can deform one CT scan based on the deformable registration file: so far, I managed to extract the deformation vector field from the dicom…
Maan
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Dicom data training failed by pytorch

I've got a problem about training the Pytorch models. I'm trying to train my Pytorch model using dicom data and nifti GT However, the size of the weight file is ridiculously small because model training is not performed normally. I used network…
mono
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How Do I Define the Name 'X_train' to create a Support Vector Machine Model from a Image Classification Tutorial?

Hello StackOverflow Community, I hope you are all doing well. I am new to the Stack Overflow Community. Here is my question. I have been recently trying to complete this Image Classification Tutorial found here (URL:…
Darrell Robinson
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SimpleITK cannot show image

I have below code. print(image.GetDimension()) works and prints the output (512, 512, 17). But sitk.Show(image) doesn't work. My Code import SimpleITK as sitk path = "C:/Users/myUserName/Desktop/0001.DCM" image =…
H42
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Medical imaging with tcia data

I'm trying to build CNN network for MRI data from tcia dataset. However, transferring DICOM format to nifti format is not working after using dicom2nifti. The coding did worked, but did not gave a file. Is this is because of the data format from…
curtis sohn
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How to superimpose segmentation result over other image

I have the original image and its segmented mask. My task is to get a colored segmentation plot over the original image. I tried following this, but it gives me the same output as the input image. import skimage.filters.rank import…
AMANDEEP KAUR
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Generating spatially correlated statistical noise using autocorrelation and python

I’m trying to emulate the methodology described in this paper: http://www.ajnr.org/content/34/8/1506 under the heading “Noise Addition to Simulate Dose Reduction” As far as I understand the authors basically completed the following steps. First,…
user3220072
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Transpose 3-D MRI image axis to different image view

How can I transpose 3D MRI image with SimpleITK to new image view, but keep aspect ration as it was in the initial view? Here is my code: def show_n_slices(array, start_from=0, step=10, columns=6, figsize=(18,10)): """ Plot N slices of a 3D…
CodingAddict
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How to convert binary file to Nifti?

We are sending data from a webpage to a python server with Json and we are trying to make predictions on the medical images. The images are supposed to be saved in .bin format. Would it be possible to convert the binary files into .nii?
Corina Holom
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how to open dicom image using fastai?

I am working on Dicom images using pydicom. But my project is in fasai and I want to open that Dicom image using the fastai library. In fastai, we normally do open_image(path) its work fine for png or jpg but if we have Dicom images we have no…
Engr Ali
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