niftiread niftiwrite cycle inappropriately changes image orientation

Hello, 

I have neuroimaging files which I have exported from Slicer as NIFTI files.

The following code snippet should produce outputImage.nii as an exact copy of inputImage.nii, but it does not.

filename = 'inputImage.nii'
im = niftiread(filename);
info = niftiinfo(filename);
niftiwrite(im,'outputImage.nii',info)

When I load outputImage.nii in Slicer, it is shown in a different orientation and location as inputImage.nii. I have found Slicer to be extraordinarily reliable for importing and exporting medical imaging data properly, so I do not think there is any error in Slicer. Even if there were, MATLAB should not have introduced any changes between inputImage.nii and outputImage.nii, so there is still evidence of a problem in MATLAB's functions even if there were a problem with Slicer.

Answer 1

[Devineni Aslesha]

Hi Randolph,

I have heard that the issue with niftiwrite function is known and the concerned parties may be investigating further.

[Ignacio]

Hi Devineni, has there been an update on this?

[Devineni Aslesha]

Hi Ignacio,

niftiwrite orientation issue might be solved in MATLAB R2020b.