Project-MONAI / Project-MONAI/tutorials
numpy.linalg.LinAlgError: Matrix is not positive definite
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Description
what is this error about? I am getting this error while performing resampling over skull-striped MRI. the code is following:
import monai
import numpy as np
from monai.transforms import LoadImage, Spacing, Compose
# Set the file path to your medical image
image_file_path = r"D:\dataset\01_brainMaskedByDL.nii"
# Use MONAI's LoadImage transform to load the image
loader = LoadImage(image_only=True)
image = loader(image_file_path)
# Print information about the original image
print("Original image shape:", image.shape)
# print("Original image spacing:", loader.metadata["spacing"])
# Set the target spacing for reslicing along the axial dimension
target_spacing = (1.5, 1.5, 3.0) # Adjust these values according to your requirements
# Use MONAI's Spacing transform for reslicing
reslicer = Spacing(target_spacing, mode="bilinear")
resliced_image = reslicer(image)
# Print information about the resliced image
print("Resliced image shape:", resliced_image.shape)
# print("Resliced image spacing:", reslicer.metadata["spacing"])
# Optionally, you can visualize the original and resliced images
import matplotlib.pyplot as plt
# Plot a single slice from the axial dimension for both the original and resliced images
original_slice = image[image.shape[0] // 2, :, :]
resliced_slice = resliced_image[resliced_image.shape[0] // 2, :, :]
plt.subplot(1, 2, 1)
plt.imshow(original_slice, cmap="gray")
plt.title("Original Image (Axial Slice)")
plt.subplot(1, 2, 2)
plt.imshow(resliced_slice, cmap="gray")
plt.title("Resliced Image (Axial Slice)")
plt.show()
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First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
Research direction
Start by reproducing the provided Python script with the referenced skull-stripped MRI and inspect the failure during the MONAI Spacing transform. Read the LoadImage and Spacing entry points and determine what input or resampling condition produces the LinAlgError; done means explaining the cause and identifying a verified resolution.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- numpy, python
- Domain
- computer-vision
- Issue type
- Bug
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 25/100