Manual change of the orientation of a 4D image since realignment

Dear Dr. Yan,

Because the normalized EPI was inaccurately aligned to the MNI standard space, I manually changed the orientation of a 4D image (.nii) after realignment (in the folder of FunImgAR). Then the resulting image was better aligned to MNI standard template then smoothed successfully. I found there was a reorientation matrix along with a 4D image in each process (e.g., in one of folder stored smoothed data from my subjects: 'swraASD01_5265.mat' & 'swraASD01_5265.nii'). Then I used the smoothed image for other preprocessing pipeline, but the results turned out to have failures in demonstrating the correct orientation. I wonder if there is a way to directly incorporate the reorientation matrix into the 4D image (writing the transformation information onto header?).

Thank you very much.

Best,

Hsiang-Yuan