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

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  2. Comment on the issue to say you are picking it up — it saves two people doing the same work.
  3. Fork the repository and make your change on a branch.
  4. 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

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