Here's a much more succinct approach for creating a 3D MKV file
So since they just released a new, allegedly very impressive (from Ralph's review) version of Gravity with an Atmos soundtrack yet failed to also make it a 3D version, I want to take the 7.1 True HD track with Atmos on it and mux it with the 3D MKV video file.
I'd like to figure out and detail the process here so that anyone who wants to do the same can do so with ease.
The first problem is finding something that will rip just the Atmos audio track (MakeMKV won't let you just rip audio) and then software that can merge the audio and video files AND that can handle not only Dolby True HD but one that knows how to handle ones that are encoded with Atmos. And, no, they're not one and the same. If they were then I'd be able to listen to Atmos on my Plex HT but I can't.
So we've got one method from Manni01 that he tested with I, Frankenstein that he got to work (only on one of his players though):
Use tsmuxer to create an ISO from an MVC mkv of the 3D version, created with makemkv, and the Atmos soundtrack from the Japanese 2D version.
This worked fine, but was only playable with TMT, not PDVD. It might be playable on a 3D mediaplayer but my Dune Base 3.0 and my NeoTV 550 are 2D only, so I couldn't test.
Tsmuxer can rip the Atmos audio straight from the disc in the drive as long as ANYDVD is enabled. (Will DVDFAB also work?)
A more detailed step-by-step (again, from Manni01):
Here is a step-by-step that works for me (you need to have AnyDVDHD running in the background).
Important note/disclaimer: you need to own the original bluray of both the 3D and 2D version, otherwise what you are doing is illegal. It might still be illegal in your country even if you own both discs, so please check you local copyright laws, etc). The point here is to try to help legal owners of the two versions to watch a combined version of the movie until a proper 3D + Atmos version becomes available to purchase, not to encourage or condone piracy):
1) Use makemkv to make an MVC mkv rip of the 3D Bluray. The playlist to select is the one with the MVC video track. Select as many audio and subtitle tracks as you want.
2) Once you have an MVC mkv of the 3D Bluray, try it in your mediaplayer. If you have PDVD or TMT on a PC, none of them support MVC files properly, so don't waste your time. TMT doesn't play them at all, and PDVD will play them as a 2D movie converted to 3D, with black borders, so pointless. The only option on a PC able to play an MVC file properly AND bitstream the dolby Atmos track is stereoscopic player. It's unfortunately not an option with an AMD GPU due to the left eye delay bug I mentioned earlier, unless you have Windows 7 or earlier and can use Catalyst 12.3 or earlier. AFAIK
it was the last version without the bug. With NVidia or Intel GPU, stereoscopic player should work, but you need to check, I only have an AMD 3D platform.
If your player supports MVC playback properly, you have now two options: keep the file as an MVC MKV and simply add the Atmos track with MKVToolnix, or do what you have to do if your player can't play MVC files properly, which is to convert the MVC back to a 3D BD ISO using tsmuxer.
3) In any case, use BD Info to identify the correct playlist on the 2D disc with Amos (from the original physical disc, no need to create an ISO first although it will work with an ISO or folder rip). If BD Info gives you too many options you can look at the disc.inf file created by anydvdhd in the structure of the bluray, the last line will tell you the valid file(s). You're obviously looking for the playlist with a dolby TrueHD track (there will be no mention of Atmos until tools are updated to identify the extra metadata, which is unlikely to happen any time soon).
4a) If your player is compatible and plays MVC files properly and if you want to keep the movie in mkv format, use mkvtoolnix to import the 3D MVC file and the 2D Atmos playlist from the physical BD reader, and create a 3D MVC file with both the 3D video and the Atmos (TrueHD) track. You'll have to deselect the 2D Video, and the non atmos tracks/subtitles that you don't want to keep. You might also move the Atmos track up so that it's selected by default in the new MVC file.
4b) If your player is unable to play MVC files properly or if you'd rather have an ISO version of the 3D Atmos movie, use tsmuxer to import the 3D MVC file and the 2D Atmos playlist from the physical BD reader, and create a BD ISO with both the 3D video and the Atmos (TrueHD) track. You'll have to deselect the 2D Video, and the non atmos tracks/subtitles that you don't want to keep. You might also move the Atmos track up so that it's selected by default in the new MVC file. The resulting ISO is only playable on my system by the standalone version of TMT (latest 6.5 in my case). It might be playable by other mediaplayers or software players, I haven't tested.
5) Cross your fingers that audio and video will be in sync, and enjoy a 3D version of your movie with a Dolby Atmos track
Using mostly step 4b above, I was successfully able to make a 3D ATMOS ISO of Gravity using tsmuxer to mux the video files (MVC and H.264, from a 3D MKV file I had already ripped) with the True-HD Atmos track from an ISO of the disc I mounted on a clone drive using the (sheep) Virtual CloneDrive. To get the audio track, when you are adding files in the upper window of tsmuxer, you go to the clone drive, in my case K, and navigate to K:\BDMV\PLAYLIST\00098.mpls. From there you select the TRUE-HD audio codec in the lower window.
I've attached a picture of what my tsmuxer window looked like to make the ISO. It plays flawlessly. As you can see, the files from the two different discs are the exact same length. I am playing it on a KDLinks HD720 Media Player. Can't guarantee that it'll work on everything.
I went with the ISO approach because installing all the necessary components for mkvtoolnix to run seemed a bit daunting. On the other hand, tsmuxer was an all-in-one solution with a GUI.
Good luck everyone!
Here is some info from Batiatus Rules on making it into an MKV:
For now, and for my purposes, I simply used MakeMKV to rip both the 3D Blu-ray and the 2D Atmos Blu-ray into MKVs. Then opened MKVToolNix and muxed the 3D MVC video, chapters and subtitles from the first MKV with only the TrueHD7.1/Atmos audio track of the second MKV. Took about 25 minutes to compile and I have 1 perfect 3D MVC MKV Atmos file. No sync issues, no playback issues in Kodi 14/15 and just in fact finished watching it and it looked fantastic and sounded amazing!