Niftiwrite - how to set orientation?
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Hi,
I am combining two MRI images on matlab and I rewrote the combined image into a niftifile using niftiwrite command. However the new image lacked orientation and coordinate when I opened in image viewer software (FSLeyes).
Can somebody suggests how to fix this issue? Thank you.
2 个评论
Walter Roberson
2023-2-13
permute() the volume data before writing it?
Jacob Bunyamin
2023-2-14
回答（1 个）
Abhijeet
2023-3-8
Hi Jacob,
To fix the issue with the orientation and coordinate information missing in the combined MRI image that you wrote into a niftifile using the niftiwrite command in MATLAB, you can follow these steps:
- Load the combined MRI image and the original MRI image that you used to create the combined image into MATLAB.
- Use the "niftiinfo" function to extract the header information from the original MRI image. This header information contains the orientation and coordinate information that is missing in the combined image.
- Copy the header information from the original MRI image to the combined image using the "niftiwrite" function with the 'Header' argument.
- Save the combined image with the corrected header information to a new niftifile.
You can try this code :
% Load the original MRI image and the combined MRI image
original_image = niftiread('original_image.nii');
combined_image = imread('combined_image.nii');
% Extract header information from the original image
original_header = niftiinfo('original_image.nii');
% Copy header information to the combined image
niftiwrite(combined_image, 'fixed_combined_image.nii', 'Header', original_header);
This code should fix the issue with the missing orientation and coordinate information in the combined image.
Thank You
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2023-2-13
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