重采样nii文件，插值法

大路诗人路小果

于 2023-07-04 19:16:32 发布

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文章标签：人工智能 python pytorch

本文链接：https://blog.csdn.net/a14285700/article/details/131541218

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重采样nii文件，插值法

原来的nii文件是（869，869，120），spacing为（0.3795，03795，1.7） 现在要转化成（340，340，204），spacing为（1，1，1）的文件
（869，869，120）.*（0.3795，03795，1.7）=（329.78，329.78，204）约等于（340，340，204）

import os
import torch
import torch.nn.functional as F
import nibabel as nib
import numpy as np

def resample_image(image, new_shape, new_spacing):
    # Move tensors to the GPU device
    device = torch.device("cuda" if torch.cuda.is_available() else "cpu")
    tensor = torch.from_numpy(image.get_fdata()).unsqueeze(0).unsqueeze(0).float().to(device)

    # Calculate the resize factor
    current_shape = tensor.shape[-3:]
    resize_factor = [n / o for n, o in zip(new_shape, current_shape)]

    # Perform the resampling using interpolate function
    resampled_tensor = F.interpolate(
        tensor,
        size=new_shape,
        mode='trilinear',
        align_corners=False
    )

    # Create a new NIfTI image with updated data and spacing
    resampled_nifti = nib.Nifti1Image(resampled_tensor.squeeze().cpu().numpy(), affine=image.affine)

    # Update the affine matrix for the desired spacing
    current_spacing = image.header.get_zooms()[:3]
    scale_factor = [c / (r * rf) for c, r, rf in zip(current_spacing, new_spacing, resize_factor)]
    resampled_nifti.header.set_zooms(new_spacing + (image.header.get_zooms()[3:]))

    # Scale the affine matrix
    resampled_nifti.affine[:3, :3] = np.diag(scale_factor)

    return resampled_nifti

# Define the path to your NIfTI file
nifti_path = r"D:\BaiduNetdiskDownload\A\P0.nii.gz"

# Load the NIfTI image
image = nib.load(nifti_path)

# Define the desired shape and spacing for resampling
new_shape = (340, 340, 204)
new_spacing = (1.0, 1.0, 1.0)

# Perform resampling
resampled_image = resample_image(image, new_shape, new_spacing)

# Define the new file name and path
output_dir = os.path.dirname(nifti_path)
output_filename = "resampled.nii.gz"
output_path = os.path.join(output_dir, output_filename)

# Save the resampled image to the new file path
nib.save(resampled_image, output_path)

print("Resampled image saved to:", output_path)