dcm2mnc and JPEG compression

[andrewjanke]

I note that dcm2mnc will silently fail on images with JPEG compression (you get black/blank images). Specifically ones that say things like this:

# Dicom-Data-Set
# Used TransferSyntax: JPEG Lossless, Non-hierarchical, 1st Order Prediction

I recognise that this is a licencing thing, meaning we'd have to include a JPEG licence in dcm2mnc to make this happen but am curious if others have ways around this. OSIRIX is one way, fork a decode process to something else?

For now I do something like this:

for i in ls -1 *.dcm; do dcmdjpeg $i unjpg/$i; done

And then the conversion is all fine. Can we link/call/something dcmdjpeg?

[rdvincent]

There is actually some code in there now to handle jpeg compression, and to crash if the compression is something we don't know how to handle. There are open-source libraries for most of the useful transfer encodings.

[andrewjanke]

Ah, in the develop branch. 157d053 I shall give it a whirl. a

…

On 5 May 2017 at 12:15, Robert D Vincent ***@***.***> wrote: There is actually some code in there now to handle jpeg compression, and to crash if the compression is something we don't know how to handle. There are open-source libraries for most of the useful transfer encodings. — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#67 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AATwipIPdNHqMzdFpjFR_T3SffIsCMvmks5r2oYwgaJpZM4NRZRD> .

[vfonov]

fixed by 157d053