Thanks @Thomas_do
May I ask the name of your HEX editor?
It’s GHex (under Linux)
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It sounds like: a) you prefer darktable and b) that you do have access to other tools. Would it be possible to batch process your old NEF’s using another tool and export as TIFF and then use darktable to do any subsequent processing - allowing you the tool of choice for editing? Just a work around thought…
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Thanks 
Thanks @grsnovi
A) Its not that I prefer Darktable, but it enables me to batch make images with their file name as watermark, a feature I have not been able to imitate in rawTherapee
If anyone knows a Linux way to do that outside Darktable, I’m all ears 
B) Running ubuntuStudio 20.04 I have access to more tools than I know how to use
If it ends up not being a problem that can be fixed, to the benefit of all D3100 shooters, changing Darktable, I thought of a similar work around, but that would be more cumbersome, and only fix my problem…
Thanks @paperdigits
Looks like ImageMagick can do watermarks as well as Darktable, but without the GUI of the later…
G’MIC can do it as well.
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Again, Phil Harvey’s utility I pointed to specifically fixes NEF files corrupted by Nikon Transfer. Still no feedback whether it worked or not…
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I could not agree more @paulmiller
It doesn’t look good when Nikon’s software partly ruin the NEFs of their paying costumers…
But maybe this doesn’t for those who stay within the world of Nikon software?
Sorry did not get around to trying it out yet, lost the thread for a moment when I was convinced it wasn’t a NEF problem…
Will have a closer look as soon as time allows.,
From Fix Corrupted Nikon NEF Images
[Note that Nikon doesn’t learn from their mistakes, and a similar problem happened 2 years earlier with an older version of Nikon Transfer and the D5000 (read here), and the new Nikon NX-D software has other corruption issues. The moral is: Don’t use Nikon Transfer or any other utility that modifies the file to download your precious images!]
It is very sad that this Nikon software bug penalizes only loyal Nikon owners (since it affects only people who had an older copy of the Nikon software from a previous camera), yet Nikon customer support provides no help other than suggesting that you contact your memory card manufacturer to see if the original images can be restored.
I tried it on the OP’s file and it didn’t create a fixed file using either 12 or 14 as input. It did create a fixed folder but the folder was empty, so I wasn’t able to test that a fixed file would subsequently open in DT.
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@grsnovi Thanks. It might just be silently failing, D3100 isn’t explicitly listed on that page.
@Soren_Garup I’d send your sample to Phil Harvey to try to include in the supported list, I venture it’s not very different to other models’ problems.
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Problem solved!
I converted the old NEFs to PGN 8 bits in rawTherapee and then ran the new PNGs through my normal darktable workflow…
Thanks to everyone, for all the good advice…
Have a good weekend
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ViewNX definately changes NEF files, but I don’t think the resulting files are corrupted. ViewNX reads them just fine (as do lots of other software packages). I think that from Nikon’s point of view the ‘MM’ variant NEF files are valid NEF files. Its just that most software that reads NEF files is based on reverse engineering camera files because Nikon have not released the NEF file specification.
You can also recover the files by passing them through Adobe DNG convertor (not free software though).
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Thanks @paulmiller for the DNG tip, but as you mentioned it strands me with NON open raw specifications, just like Nikon’s NEF…
There is openRAw, but it seems like it has been abandoned years ago?
Great project though
The DNG format is completely public, so there are no ‘openness’ or vendor lock-in issues associated with it. Only the DNG Converter is proprietary.
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Last time I looked into the DNG format and I admit it was years ago, it didn’t seem like it was very popular in Linux communities…,
Maybe for the reason’s mentioned by @kmilos
On the other hand the completely open alternative mentioned earlier OpenRaw, seemed abandoned…