Hi Felix,<div><br></div><div>Not entirely sure why this would happen, but I'm guessing these are Siemens data? SV10 refers to the format they use to store their CSA data within the DICOM stream. The only time I've had that particular error is when trying to read images stored using the newer DICOM multi-frame format. My suggestion would be to install the patch that I released a few weeks ago implementing support for multi-frame, which might also sort out a few other issues. You can get the patch here: <a href="http://www.nitrc.org/pipermail/mrtrix-discussion/2012-September/000528.html">http://www.nitrc.org/pipermail/mrtrix-discussion/2012-September/000528.html</a>. <br>
<br>For some reason, the NITRC mailing list backend seems to have removed all the text from that message and left only the attachment. Here's the original text with the installation instructions:</div><div><br></div>
<blockquote style="margin:0 0 0 40px;border:none;padding:0px">
<div><span style="color:rgb(34,34,34);font-family:arial,sans-serif;font-size:15px;background-color:rgb(255,255,255)"><i>Dear MRtrix users,</i></span></div><div><div style="color:rgb(34,34,34);font-family:arial,sans-serif;font-size:15px;background-color:rgb(255,255,255)">
<i><br></i></div></div><div><div style="color:rgb(34,34,34);font-family:arial,sans-serif;font-size:15px;background-color:rgb(255,255,255)"><i>I've had a few requests recently about DICOM multi-frame support, so I've finally done something about it. Attached is a patch implementing this, which should apply cleanly against the current 0.2.10 source download. I'm releasing it now as a patch since it required a fairly extensive rewrite of the DICOM backend in MRtrix, and the chances are there will be a few bugs that remain to be sorted out. That said, I've tried it out on a few datasets from a range of manufacturers, and so far it seems to work OK for both multi-frame and "traditional" DICOM data. It might also solve a few issues others have reported recently when trying to extract the diffusion information. </i></div>
</div><div><div style="color:rgb(34,34,34);font-family:arial,sans-serif;font-size:15px;background-color:rgb(255,255,255)"><i><br></i></div></div><div><div style="color:rgb(34,34,34);font-family:arial,sans-serif;font-size:15px;background-color:rgb(255,255,255)">
<i>So I'd be grateful if people could give this a go, both for standard and multi-frame DICOM data, and send me feedback about what works and what doesn't (hopefully not much). Once I'm happy everything works OK, I'll put out a new proper release. </i></div>
</div><div><div style="color:rgb(34,34,34);font-family:arial,sans-serif;font-size:15px;background-color:rgb(255,255,255)"><i><br></i></div></div><div><div style="color:rgb(34,34,34);font-family:arial,sans-serif;font-size:15px;background-color:rgb(255,255,255)">
<i>To install the patch, dump it in your MRtrix source folder, and issue the following commands (as per usual, amend as necessary):</i></div></div><div><div style="color:rgb(34,34,34);font-family:arial,sans-serif;font-size:15px;background-color:rgb(255,255,255)">
<i><br></i></div></div><div><div style="color:rgb(34,34,34);font-family:arial,sans-serif;font-size:15px;background-color:rgb(255,255,255)"><i>$ cd mrtrix</i></div></div><div><div style="color:rgb(34,34,34);font-family:arial,sans-serif;font-size:15px;background-color:rgb(255,255,255)">
<i>$ tar xvfj mrtrix-0.2.10_DICOM_multiframe_patch.tar.bz2 </i></div></div><div><div style="color:rgb(34,34,34);font-family:arial,sans-serif;font-size:15px;background-color:rgb(255,255,255)"><i>$ ./build</i></div></div><div>
<div style="color:rgb(34,34,34);font-family:arial,sans-serif;font-size:15px;background-color:rgb(255,255,255)"><i>$ sudo ./build install</i></div></div><div><div style="color:rgb(34,34,34);font-family:arial,sans-serif;font-size:15px;background-color:rgb(255,255,255)">
<i><br></i></div></div><div><div style="color:rgb(34,34,34);font-family:arial,sans-serif;font-size:15px;background-color:rgb(255,255,255)"><i>Cheers,</i></div></div><div><div style="color:rgb(34,34,34);font-family:arial,sans-serif;font-size:15px;background-color:rgb(255,255,255)">
<i><br></i></div></div><div><div style="color:rgb(34,34,34);font-family:arial,sans-serif;font-size:15px;background-color:rgb(255,255,255)"><i>Donald.</i></div></div></blockquote><div><br></div><div><br></div><div>Let me whether or not this fixes the problem.</div>
<div>Cheers,</div><div><br></div><div>Donald.</div><div><br></div><div><div class="gmail_quote"><br></div><div class="gmail_quote"><br></div><div class="gmail_quote">On 23 October 2012 08:10, Félix C. Morency <span dir="ltr"><<a href="mailto:felix.morency@gmail.com" target="_blank">felix.morency@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Hi,<br>
<br>
I am trying to convert some DICOM files using mrconvert but have the<br>
following error:<br>
<br>
mrconvert [DEBUG]: file "./IM000008" mapped at 0x7f3177e0f000, size<br>
155050 (read-only)<br>
mrconvert: CSA data is not in SV10 format<br>
mrconvert [DEBUG]: unmapping file "./IM000008"<br>
mrconvert: error reading series 3 of DICOM image "Patient #4 [MR]<br>
AXIAL SE T1"<br>
mrconvert: error opening image "."<br>
mrconvert [INFO]: closing image "."...<br>
<br>
I'm using MRtrix 0.2.10, glib 2.32.3, GSL 1.15<br>
<br>
Does anyone knows why this happens?<br>
<br>
Regards,<br>
--<br>
Félix C. Morency, M.Sc.<br>
Plateforme d’analyse et de visualisation d’images<br>
Centre Hospitalier Universitaire de Sherbrooke<br>
Centre de recherche clinique Étienne-Le Bel<br>
Local Z5-3031 | 819.346.1110 ext 16634<br>
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</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>
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