251 questions
Advice
0
votes
3
replies
31
views
Finding microns per pixel of tissue slide sample for ML
I'm building ensemble of convolutional neural networks for identifying different types of cancer stages and properties from tissue slide samples. I have multiple datasets with different magnification ...
- 97
Best practices
0
votes
1
replies
14
views
How to find a resource file with pyaims using the BrainVISA suite of software?
Using the recently released BrainVISA, a neuroimaging suite of software (https://brainvisa.info/), version 6.0.1, installed using pixi, I would like to access the resource template files (like the ...
- 449
0
votes
0
answers
46
views
Proper utilization of sliding window inferer
I am training an Encoder-Decoder network to reconstruct brain CT images. Due to OOM (Out of Memory) errors with full-sized images, I implemented a sliding window approach for training and inference.
...
- 3
1
vote
1
answer
151
views
How to enable progressive loading of NIfTI images?
I am trying to display a NIfTI image in CornerstoneJS while progressively loading it from a backend URL. The backend exposes a URL to download the NIfTI file, and I want to visualize slices ...
- 729
2
votes
0
answers
70
views
kernel died when I run : dataset = Dataset.from_dict(data_dict)
I am fine-tuning sam model for my dataset containing train_images and train_masks. I am able to create dict, but when calling last command i.e. to load dataset from dict, kernel dies. It happened ...
- 21
0
votes
1
answer
326
views
How to resample anisotropic voxel size (CT) into isotropic voxel size
I am working on a code to standardize voxel sizes of 3D Dicom series from multiple machines (as part of a pipeline, but for now we'll focus on voxel sizes). It needs to be able to handle input of both ...
- 1
1
vote
0
answers
72
views
How to reconstruct an image from s-parameters in MATLAB with datasets are 37 files colleting from 0-360 degree angle (10 degree of increment)?
How to reconstruct an image from s-parameters in MATLAB ? My dataset are 37 files colleting from 0-360 degree angle (10 degree of increment), all data collected from VNA
I have a set of data which is ...
- 11
0
votes
0
answers
96
views
Calculate the inner contour of a computed tomography
I'm working on a project to calculate the level of a chest deformity.
For that, I need to find the inner contour of the chest from the tomography; however, I don't know how to select the inner contour....
- 41
1
vote
1
answer
306
views
Get 3D affine transformation matrix from mri DICOM files
I have both RTDose and MRI information in DICOM format. Unfortunately raw MRI and RTDose files share not only different dimensions but incompatible actual spacing as well.
Looking Here I've been ...
- 13
0
votes
1
answer
53
views
ITK ERROR: MaskNegatedImageFilter(000001D7CB479830): Inputs do not occupy the same physical space
I used a code to compute the 95HD and DSC to assess the segmentaion accuracy of medical image, and the following problem appered "ITK ERROR: MaskNegatedImageFilter(000001D7CB479830): Inputs do ...
- 35
0
votes
1
answer
121
views
Various combination of model predictions yields to similar ground truth
I have a model(3DUnet, Regression problem) that predicts values PD and T1, where PD and T1 are the qMRI outputs based on the input. From these predictions, I calculate T1_Weighted_image using the ...
2
votes
1
answer
421
views
Which DICOM Tag should we use to differentiate between the series?
We've been working on DICOM datasets for a while and we have the following problem right now. We have been dealing with the Prostate-MRI case and we have the difficulty to distinguish between ...
- 23
0
votes
0
answers
55
views
MATLAB get peak values from second x axis
I´m currently trying on overlaying DICOM echo and CT images based on ECG time and 3 landmarks. The ECG line is within the echo image and I have extracted it from the echo image based on color and it ...
- 1
0
votes
1
answer
175
views
Why does import of S3 "sub-bucket" into HealthImaging fail with "no file matches S3 URI" error?
While attempting to import programmatically a specific "subdirectory" of DICOM objects from an S3 bucket into a HealthImaging data store, I'm getting a "No file matches the provided ...
- 1
0
votes
0
answers
178
views
Implementing Interactive 3D Visualization with DICOM Series, Volume Rendering, and STL Model Integration using VTK and Qt
I'm currently working on a medical imaging project where I need to implement interactive 3D visualization using DICOM series, volume rendering, and integrate an STL model representing a screw into the ...
