<html dir="ltr">
<head>
<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1">
<style type="text/css" id="owaParaStyle"></style>
</head>
<body fpstyle="1" ocsi="0">
<div style="direction: ltr;font-family: Tahoma;color: #000000;font-size: 10pt;">Hi,
<div>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.<br>
<div style="font-family: Times New Roman; color: #000000; font-size: 16px">
<hr tabindex="-1">
<div id="divRpF782265" style="direction: ltr; "><font face="Tahoma" size="2" color="#000000"><b>From:</b> mrtrix-discussion-bounces@www.nitrc.org [mrtrix-discussion-bounces@www.nitrc.org] on behalf of Donald Tournier [d.tournier@brain.org.au]<br>
<b>Sent:</b> Wednesday, May 08, 2013 1:12 PM<br>
<b>To:</b> Hugh Pemberton<br>
<b>Cc:</b> mrtrix mailinglist<br>
<b>Subject:</b> Re: [Mrtrix-discussion] Fwd:<br>
</font><br>
</div>
<div></div>
<div>
<div dir="ltr">Hi Hugh,
<div><br>
</div>
<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>
<div style=""><br>
</div>
<div style="">That said, I'd be happy to help if anyone wants to try coding up support for JPEG... </div>
<div style=""><br>
</div>
<div style="">Sorry I can't be more help...</div>
<div style="">Cheers,</div>
<div style=""><br>
</div>
<div style="">Donald.</div>
<div style=""><br>
</div>
<div style=""><br>
</div>
</div>
<div class="gmail_extra"><br>
<br>
<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>
<div class="gmail_quote">
<div dir="ltr">
<div><br>
</div>
<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>
<div>
<div style="font-family:arial,sans-serif; font-size:13px"><br>
</div>
<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>
</div>
<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>
</div>
</div>
</div>
<br>
</div>
<br>
_______________________________________________<br>
Mrtrix-discussion mailing list<br>
<a href="mailto:Mrtrix-discussion@www.nitrc.org" target="_blank">Mrtrix-discussion@www.nitrc.org</a><br>
<a href="http://www.nitrc.org/mailman/listinfo/mrtrix-discussion" target="_blank">http://www.nitrc.org/mailman/listinfo/mrtrix-discussion</a><br>
<br>
</blockquote>
</div>
<br>
<br clear="all">
<div><br>
</div>
-- <br>
<font color="#ff6600" size="1"><b>Dr Jacques-Donald Tournier<br>
</b></font>
<div><font color="#ff6600" size="1">Research Fellow</font></div>
<div><font size="1"><br>
</font></div>
<div><font size="1">The Florey Institute of Neuroscience and Mental Health</font></div>
<div><font size="1">Melbourne Brain Centre - Austin Campus</font></div>
<div><font size="1">245 Burgundy Street</font></div>
<div><font size="1">Heidelberg Vic 3084</font></div>
<div><font size="1">Ph: +61 3 9035 7033</font></div>
<div><font size="1">Fax: +61 3 9035 7307</font></div>
<div><font size="1"><a href="http://www.florey.edu.au" target="_blank">www.florey.edu.au</a></font></div>
<br>
</div>
<br clear="both">
______________________________________________________________________<br>
This email has been scanned by the Symantec Email Security.cloud service.<br>
For more information please visit http://www.symanteccloud.com<br>
<br>
If you have any question, please contact MCRI IT Helpdesk for further assistance.<br>
______________________________________________________________________<br>
</div>
</div>
</div>
</div>
<br clear="both">
______________________________________________________________________<BR>
This email has been scanned by the Symantec Email Security.cloud service.<BR>
For more information please visit http://www.symanteccloud.com<BR>
______________________________________________________________________<BR>
</body>
</html>