What tool are you using to view the NIfTI data? You should request that they update the tool to use the NIfTI s-form and correctly orient the image. I suspect the viewing tool you are using is displaying the NIfTI image just as a DICOM image. By default, DICOM 2D slices are shown with the first line at the top of the screen and the last line at the bottom of the screen, in the same order we read English. In contrast, by default NIfTI 2D images are stored to disk with the first line at the bottom of the screen and the last line at the top of the screen - the same way we draw a graph with cartesian coordinates where the Y axis increases as we move up. 
  https://www.nitrc.org/plugins/mwiki/inde...
Viewing software needs to take this into account. Ideally, the viewing software will also use the spatial transforms to orient your images correctly.