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My system has 11 speakers (including 4 in the ceiling) + 1 subwoofer.
Can I rip blurays that have Dolby Atmos sound to 11.1? The audio track is always TrueHD Surround 7.1, with the TrueHD Atmos codec.
Thanks

MakeMKV does not care what your system can do. It just rips the video.

I am not aware of discrete channel encoding above 7.1 (or I think technically 7.1.4), but I never claim to be all-knowing.
However, I read some years ago regarding the newer audio processing of Dolby Atmos & DTS:X.
If you are not familiar with them or how they function, I suggest reading on them.
I suspect you are thinking in a traditional "discrete audio channel" style where each sound is specified to be emitted from 1 or more specific speakers.
Brief description of Dolby Atmos & DTS:X is they are spatial audio, not traditionally discrete.
Spatial audio allows sounds to move more naturally around you and is not mixed in discrete channels as all prior audio (think Dolby 5.1, etc) was.
While I do not presently remember the exact values, I remember 1 of Atmos & DTS:X was able to use up to 16 channels (I think it was Atmos) while the other could use many more (probably DTS:X, I remember reading both 32 & 128, but 128 was probably for professional cinemas).
The summary is you need not think as you are in trying to encode discrete 11.1 audio because Atmos & DTS:X will use as much as you have up to what they are capable, so you merely need to ensure you rip those and do not transcode them to any lesser format.

Oh, and I forgot to clarify what you said.
You have 11 speakers + 1 subwoofer, but 4 of your speakers are in the ceiling?
That is not an 11.1 sound system, that is actually 7.1.4.
The 1st # refers to the traditional thinking of speakers & surround being on your horizontal plane. Think: at the same height as your head.
The 2nd # refers to your subwoofers, 1 being most common with 2 being much less common, and 2 is the most I am aware of most audio processing being able to use outside of very custom sound setups.
The 3rd # refers to vertical speakers, being those in the ceiling or upward-facing to give the 3rd-dimension of height to your audio.
So of your 11 speakers with 1 subwoofer, the 4 in the ceiling would be shifted from the 1st # to the 3rd #, hence 7.1.4.
Definitely research spatial audio and don't try to recode Atmos or DTS:X.
When you see Atmos or DTS:X audio sources listed as 7.1, that is the core audio they use, not the spatial audio.
Think of that as a single audio file which actually has 2 audio streams in it, a 7.1 core stream so systems which lack Atmos/DTS:X capability can read it & play sound, with a spatial audio stream built around it which capable systems would process to give you the full spatial audio experience.
Know both rely on lossless audio encoding, so Dolby Atmos requires Dolby TrueHD and DTS:X requires DTS-HD MA, but the reverse is not true so you can have a Dolby TrueHD audio stream which has no Atmos and DTS-HD MA which has no DTS:X.
Because of them being lossless, both TrueHD (and therefore Atmos) & DTS-HD MA (and therefore DTS:X) are very high-bitrate streams compared to prior formats and therefore much larger.
For example, Dolby Digital typically ranges from 448Kbps to 640Kbps, while TrueHD I saw vary from 4000 to 7000Kbps.
It could vary more than that, I cannot claim I checked every TrueHD or DTS-HD MA stream's bitrate or read what other people found.