Hello Ting, Can you let me know which FSL version you are using? Kind Regards Matthew > Dear FSL users, > > I am processing a batch of fMRI data which scans along x-axis, left to right. There is something off during the slice timing procedure. Here is my scripts. > > slicetimer -i func.nii.gz -o func_st.nii.gz -r 2 -d 1 > > The orientation of input (func.nii.gz) is RPI. However, output (func_st.nii.gz) is LPS. In FSLview, I found that the left/right, superior/inferior of func_st.nii.gz is opposite from func.nii.gz. > > Does anyone have experience about slice timing the sagittal acquisition EPI data? Look forward your kind help! Thanks a lot! > > Ting