The foot head issue seems to reflect the setting of the Trio data. I have very little experience with these images. For existing images, you should make sure the spatial orientation, slice timing and gradient vector direction are correct. For future acquisitions, make sure that the default image numbering is used. If you have any questions you should seek the help of the Siemens Research Collaboration Manager associated with the site where the data was acquired. I have done my best to robustly handle data from a wide array of devices, but my software will generate warnings in situations where I have do not have enough experience to provide confident conversions.