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Just a little more detail, now that I've had a chance to check.
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<div>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.</div>
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<div>On 08/05/2013, at 1:12 PM, Donald Tournier wrote:</div>
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<div dir="ltr">Hi Hugh,
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<div style="">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...?</div>
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<div style="">That said, I'd be happy to help if anyone wants to try coding up support for JPEG... </div>
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<div style="">Sorry I can't be more help...</div>
<div style="">Cheers,</div>
<div style=""><br>
</div>
<div style="">Donald.</div>
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<div class="gmail_quote">On 8 May 2013 12:47, Hugh Pemberton <span dir="ltr"><<a href="mailto:hughpemberton1@gmail.com" target="_blank">hughpemberton1@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div dir="ltr">Hi mrtrix crew,<br>
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<div>I've been using mrconvert to get my dcm files to nii for a while now <span style="font-family:arial,sans-serif;font-size:13px">
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</span>, i've used ****** to block out a patients' name which is also the directory name<span style="font-family:arial,sans-serif;font-size:13px"> -
</span></div>
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<div style="font-family:arial,sans-serif;font-size:13px">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</div>
<div style="font-family:arial,sans-serif;font-size:13px">mrconvert: scanning DICOM folder "/home/hugh....20.128.66.20120420.75751.6031595" - ok</div>
<div style="font-family:arial,sans-serif;font-size:13px">mrconvert: no DICOM images found in "/home/hughp/BH-high-res-mri/***********/1.2.124.113532.172.20.128.66.20120420.75751.6031595"</div>
<div style="font-family:arial,sans-serif;font-size:13px">mrconvert: error opening image "/home/hughp/BH-high-res-mri/***********/1.2.124.113532.172.20.128.66.20120420.75751.6031595"</div>
<div style="font-family:arial,sans-serif;font-size:13px"><br>
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<div style="font-family:arial,sans-serif;font-size:13px">Thanks and hope you can help,</div>
<div style="font-family:arial,sans-serif;font-size:13px"><br>
Best,</div>
<div style="font-family:arial,sans-serif;font-size:13px">Hugh</div>
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