[Mrtrix-discussion]

[Richard Beare]

Just a little more detail, now that I've had a chance to check.

In Osirix, when exporting dicoms, there is a "decompress" option at the bottom of the save dialog box which saves without jpeg compression. So, in principle, you should be able to import your dicoms (from files or direct from PACS) then export with this option, then convert to nifti or mif as normal.

On 08/05/2013, at 1:12 PM, Donald Tournier wrote:

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
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Fax:  +61 3 9035 7307
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Dr Richard Beare, PhD
Postdoctoral Research Fellow
Developmental Imaging
Critical Care and Neurosciences

Murdoch Childrens Research Institute
The Royal Children's Hospital
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