[Mrtrix-discussion] Fwd:

[Richard Beare]

Hi,
There is a way of side stepping this issue at the stage of downloading from PACS, and  potentially you can use the same trick if your data is not on PACS. We've used Osirix to do this when retrieving from the PACS - hidden away somewhere are options to transcode the dicoms into a non-jpeg form which you can then convert. Other clients may do the same thing. I'd also expect there to be an option to import and then export your dicoms after removing the jpeg compression, but I've never tried that. Sorry I can't be more specific - I'm not in front of the right machine at present.
________________________________
From: mrtrix-discussion-bounces at www.nitrc.org [mrtrix-discussion-bounces at www.nitrc.org] on behalf of Donald Tournier [d.tournier at brain.org.au]
Sent: Wednesday, May 08, 2013 1:12 PM
To: Hugh Pemberton
Cc: mrtrix mailinglist
Subject: Re: [Mrtrix-discussion] Fwd:

Hi Hugh,

Looks like your data are JPEG encoded. Having waded through the DICOM specifications (no fun at all), I eventually came across the bit that mentions that the ridiculously-named '1.2.840.10008.1.2.4.70' transfer syntax actually means 'lossless JPEG compression'. I'm afraid you're out of luck, since I've no plans to implement support for that any time soon. I also have a feeling that you'll have trouble finding other free software to read these data: in my (limited) experience, none of them support JPEG - I may be wrong though, maybe someone else on this list can suggest something else...?

That said, I'd be happy to help if anyone wants to try coding up support for JPEG...

Sorry I can't be more help...
Cheers,

Donald.




On 8 May 2013 12:47, Hugh Pemberton <hughpemberton1 at gmail.com<mailto:hughpemberton1 at gmail.com>> wrote:
Hi mrtrix crew,

I've been using mrconvert to get my dcm files to nii for a while now However, out the blue I started getting error messages, the first 2 lines come up heaps of times and then it ends with the last 3 lines, i've used ****** to block out a patients' name which is also the directory name -

mrconvert: unknown DICOM transfer syntax: "1.2.840.10008.1.2.4.70" in file "/home/hughp/BH-high-res-mri/***********/1.2.124.113532.172.20.128.66.20120420.75751.6031595/1.3.12.2.1107.5.2.6.14402.30000012041919563025000000476/1.3.12.2.1107.5.2.6.14402.30000012041919563025000000493.dcm" - ignored
mrconvert: scanning DICOM folder "/home/hugh....20.128.66.20120420.75751.6031595"  - ok
mrconvert: no DICOM images found in "/home/hughp/BH-high-res-mri/***********/1.2.124.113532.172.20.128.66.20120420.75751.6031595"
mrconvert: error opening image "/home/hughp/BH-high-res-mri/***********/1.2.124.113532.172.20.128.66.20120420.75751.6031595"

Thanks and hope you can help,

Best,
Hugh


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--
Dr Jacques-Donald Tournier
Research Fellow

The Florey Institute of Neuroscience and Mental Health
Melbourne Brain Centre - Austin Campus
245 Burgundy Street
Heidelberg  Vic  3084
Ph:  +61 3 9035 7033
Fax:  +61 3 9035 7307
www.florey.edu.au<http://www.florey.edu.au>


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