Performing slice timing will reorient functional images?

Hi Yan,

I found an interesting phenomenon when I perform slice timing. First, I reoriented functional and T1 images using spm before preprocessing. Then I chose slice timing, realign, reorient fun and reorient T1 in dparsfa and pressed run button. Dparsfa performed slice timing and realign first, and then performed reorient T1 images and functional images. During reorienting functional images, the images reoriented by spm became unreoriented and I need to reorient them once again. I did the process again without performing slice timing (with realign) and this phenomenon disappeared. I doubt something wrong happened during slice timing. 

I guess you only reoriented one image by using SPM?

I reoriented all the functional images and 3 T1 images of the same subject  after setting the reorient parameters.

Find if there is a .mat file after reorienting using SPM. If yes, try to delete and have a look.