The problem here is that the orientation is wrong. You need to change that with either 3drefit or to3d. 3drefit -orient is useful if you know what the correct orientation is. You should be able to get that from the scanner's parameters. If you can not get that iinformation, I find that to3d with the .BRIK or .nii file is useful for figuring out the orientation. Use something like:

to3d '3D:0:0:192:192:40:wrongorient+orig.BRIK'

Change the numbers to reflect the number of voxels in your dataset. Without the -prefix option, the to3d program will start a GUI that can guide you to find the orientation. Click the "View images" button, and note the direction across the image viewer, down the viewer and across slices. The first letters of the directions correspond to the correct orientation (RAI, for instance). Note that it will be difficult to assess left/right unless there is an anatomical or fiducial marker of some sort. Voxel size can be set there too by clicking irregular and setting the known voxel sizes. You can either save a new dataset from the to3d GUI or just use the orientation determined like this with 3drefit. Once you have the correct orientation, you can refit the header information with this command:

3drefit -orient XYZ wrongorient+orig

Instead of "XYZ", put the correct orientation.