Thanks Taylor!
Sorry, I did not express it clearly. Sure, if you want to write out the values into a file you should specify the rotated grid and interpolate values. My question is that, can you just change the information in the header so the data will be displayed as transformed in the afni gui.

Imaging that you have an epi, a t1 and the affine transform between them. I just want to display the epi file overlayed on the t1 file in the afni viewer. In this case, you do not need to resample epi data. You just need to change the header info in the epi file and the afni viewer will correctly interpret the header and transform the image such that the transformed epi and T1 are overlapped. In this case, the epi data are not touched at all and keep the same value and the same size.

In nifti files, the mapping from the voxel space to the physical (i.e., RAI) space is controlled by sform and qform. Can 3dAllineate directly change sform/qform such that only the mapping is changed but the data are untouched?

Thanks.

-rz



Edited 1 time(s). Last edit at 04/17/2019 04:26PM by ruyuanzhang.