You should find a config.ini file in the Ultimate Ninja Storm 4 folder.
Go to the location of your Steam folder (right-click Steam icon, select “Properties” and open the file location) and navigate to the Naruto Shippuden: Ultimate Ninja Storm 4 folder (steamapps -> common -> Naruto Shippuden game’s folder).
This worked fine before the new patch that was released yesterday, after the patch some people said that this fix doesn t work anymore. Then you would have to enable 3D manually after starting the game. In Windows 10 you can try this, go to services.msc and disable 'Touch Keyboard and Handwriting Panel Service'. If for some reason the game displays an "Out of memory error" at launch (it happened to me in older drivers) you can try setting "StereoDefaultOn" to 0 in "d3dx.ini". Run the game and let it overwrite the profile the first time. Download this file and extract its contents in the " NARUTO SHIPPUDEN Ultimate Ninja STORM 4" folder, where " NSUNS4.exe" is. Besides, some main menu options flicker with this. When subtitles load, they get corrupted if the HUD was at depth before they appeared. I don't recommend using the HUD depth hotkey.
Meanwhile there was one similar to them that I placed at full depth. Some patterns in some attack textures (Gaara's sand, Amaterasu flames, Shino's bugs, etc) are at screen depth. Some bloom effects can be imperfect sometimes.
Decals, thanks to something done by Schwing. A lot of double stereoization problems that made the game unplayable. I recommend just playing at higher resolution, which benefits cel shading more). Just keep in mind that the game disables decals when MSAA is enabled (not my fault. Also, the game is now playable with MSAA enabled.
We have to thank Schwing for telling me how to make them appear on both eyes.
Update (): decals are now fixed so I deleted the option to disable them. If you used a work in progress version in the past, make sure you reset the game profile with Nvidia Profile Inspector first. 3D Vision fix for NARUTO SHIPPUDEN: Ultimate Ninja STORM 4.