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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Detecting Circles with Partial Edges (MATLAB for Cell Growth on Microcarriers)
I am attempting to develop software that will determine the confluency of the cells we are producing on microcarriers. To do that you need to determine the area occupied by the cells divided by the area available for the cells to grow. So 100%…
Bigfoot Mountain
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DICOM file segmentation in Matlab. Export 4d to 3d?
I would like to segment a medical case using Image Segmenter. I know how to do this, but I need a 3D file in workspace. I am using the Dicom viewer to read the folder with the dicom files. Unfortunately, it only exports 4d. How can I turn it into…
Izabela
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Visualize SimpleITK coordinates on Paraview
I am trying to just make an SimpleITK image where I want specific voxel values to be 1 and the rest to be 0. I am new to SimpleITK so I feel I am missing out on something.
Anyway, I have some indices that I have generated that I assign the voxel…
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how to find min/max axis length across the centroid of a closed curve
I'm doing a segmentation task. Now I successfully segmented the area of interest and find the contour of the area. How can I calculate the min/max axis length of the contour? The axis does not have to be orthogonal.
What I already got…
nnzzll
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Reading header information from .mha file
I want to read only the header from a .mha file. Ideally it would give me the same as if reading .mhd file with metadata only.
I am using SimpleITK for reading and while it reads the image fine, I specifically want to create a metadata…
Jarartur
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create the pixel size for Dicom_Picture in matlab
I have pictures in .dcm format. From Dicominfo I learned that the pixel spacing is [0.9,0.9] mm and the slice thickness is 1.98 mm.
My task: I should get the picture size in real (world) coordinates and then display the pictures in all three…
Natali Graß
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Converting .nrrd Segmentation to Nifti Volume with reference volume
I have 200+ CT-Volume Files with matching segmentations. The Volumes are in .nrrd format and the segmentations are in seg.nrrd format. I need both of those as .nii.gz format and I want to script the conversion from one into the other…
Hball99
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dimensions of image read using tfio.image.decode_dicom_image
I read a .dcm image from my own dataset using tfio.image.decode_dicom_image following this link. The shape of the read image is shown as (None,None,None,None). While displaying the image using plt.imshow, the output of np.squeeze is zero-dimensional…
psj
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Performance in reading dicom files with SimpleITK and PyTorch
I want to directly load image from memory to python in pytorch tensor format.
I modified GetArrayViewFromImage() function by replacing those lines:
image_memory_view = _GetMemoryViewFromImage(image)
array_view =…
Jarartur
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Representation of values instead of colors in a 2D image
I'm looking for a command in Matlab that does not display an image with the colors, but the value for the pixel.
for example: in pixel (1,1) is black and is 0.
I just wanted to represent the value 0 in a figure.
In addition, the image is in DICOM…
Natali Graß
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Connecting discontinuous lines spinal roots
I have a project to build a 3D model of the spinal roots in order to simulate the stimulation by an electrode. For the moment I've been handled two things, the extracted positions of the spinal roots (from the CT scans) and the selected segments out…
Raphasse
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DCMTK library says tag not found while dcmdump displays it
My program, for a Ubuntu 20 system using DCMTK 3.6.4-2, reads a dicom file (series) and gets the scale slopes from the corresponding tags, testing first whether they exist:
tmpfile.loadFile ( filename );
tmpdata = tmpfile.getDataset();
tmpdata ->…
alle_meije
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Getting just a binary image of the lungs
I have a problem where I am struggling to make a purely binary mask of the lungs, where the pixel value is one inside of the lung and is a 1 outside of the lungs. I used a kmeans and otsu and a few other methods to segment the lungs. I will attach a…
Mattias Weiland
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Upload data from DICOM files in Torchvision Model
I'm sorry if the question is too basic, but I am just getting started with PyTorch (and Python).
I was trying to follow step by step the instructions here:
https://pytorch.org/tutorials/beginner/finetuning_torchvision_models_tutorial.html
However,I…
BubuSettete
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CT image preprocessing in python?
I have a 3D CT image of a car engine in raw form with no header information. When loaded into numpy array as 16 bit unsigned integer, I noticed that the values range between 0 to 52000. Is this normal for a CT Image? When viewing the image, I also…
faiz fz
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