Hi,

For the purpose of my analysis, I would like to save flipped versions of my fMRI NIfTI files. With the 2019 version of MRIcron, I have tried View, then flip L/R, and then I save that image as a new file. However, I do not think it saves the flipped version. Is there a way to do this in MRIcron?

Thank you. 

Hello,

  MRIcron is a visualization tool, not an image manipulation tool. The View/FlipLR is designed to change between neurological and radiological orientation.

You could try MRIcroGL, which has the Import/Tools/Rotation menu item.

Alternately, you could write a Python script. Here is what ChatGPT suggests:

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import nibabel as nib
import numpy as np

def flip_first_dimension(input_path, output_path):
    # Load the NIfTI file
    img = nib.load(input_path)
    data = img.get_fdata()

    # Flip the order of voxels in the first dimension
    flipped_data = np.flip(data, axis=0)

    # Create a new NIfTI image with the flipped data
    flipped_img = nib.Nifti1Image(flipped_data, img.affine, img.header)

    # Save the flipped NIfTI file
    nib.save(flipped_img, output_path)
    print(f"Flipped NIfTI file saved to {output_path}")

if __name__ == "__main__":
    # Replace 'input_file.nii.gz' and 'output_file.nii.gz' with your file paths
    input_file_path = 'input_file.nii.gz'
    output_file_path = 'output_file.nii.gz'

    flip_first_dimension(input_file_path, output_file_path)