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 inls -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.

https://github.com/BIC-MNI/minc-tools/commit/157d0532dd137e21147ee3de6a92e77f37463457

I shall give it a whirl.

a

On 5 May 2017 at 12:15, Robert D Vincent notifications@github.com 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 https://github.com/BIC-MNI/minc-tools/issues/67#issuecomment-299355491, or mute the thread https://github.com/notifications/unsubscribe-auth/AATwipIPdNHqMzdFpjFR_T3SffIsCMvmks5r2oYwgaJpZM4NRZRD .

[vfonov]

fixed by https://github.com/BIC-MNI/minc-tools/commit/157d0532dd137e21147ee3de6a92e77f37463457