<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;">
<div><span style="font-size: 10pt;">Hi all,</span></div>
<div><span style="font-size: 10pt;"><br>
</span></div>
<div><span style="font-size: 10pt;">I noticed there are quite a few people struggling with getting the gradient orientations right. As it happens,</span><span style="font-size: 10pt;"> I will be presenting a poster entitled "How to make sure you are using the
correct gradient orientations in your diffusion MRI study?" at the ISMRM meeting in Salt Lake City (</span><a href="http://www.ismrm.org/13/tp03.htm" target="_blank" style="font-size: 10pt;">http://www.ismrm.org/13/tp03.htm</a><span style="font-size: 10pt;">),
next week, which deals with this very topic. </span><span style="font-size: 10pt;">During my poster presentation, I will demonstrate a web application (with mrtrix support), which ensures that the gradient orientations are properly aligned with the DWI data. </span><span style="font-size: 10pt;">The
same presentation will also be given as the ISMRM diffusion study group meeting later that week.</span></div>
<div><span style="font-size: 10pt;"><br>
</span></div>
<div><span style="font-size: 10pt;">So all mrtrix users, facing issues with the gradient tables are kindly invited to these poster presentations!</span></div>
<div><br>
</div>
<div><span style="font-size: 10pt;">Cheers,</span></div>
<div><span style="font-size: 10pt;">Ben</span></div>
<div><br>
<div style="font-family:Tahoma; font-size:13px">
<div style="font-family:Tahoma; font-size:13px">
<div style="font-family:Tahoma; font-size:13px">
<div style="widows:2; text-transform:none; text-indent:0px; letter-spacing:normal; font:13px Tahoma; white-space:normal; orphans:2; color:rgb(0,0,0); word-spacing:0px">
<div><font size="1"></font></div>
<font size="1">Ben Jeurissen, Ph.D.</font></div>
<div style="widows:2; text-transform:none; text-indent:0px; letter-spacing:normal; font-style:normal; font-variant:normal; font-size:13px; line-height:normal; font-family:Tahoma; white-space:normal; orphans:2; word-spacing:0px">
<div style="font-weight:normal; color:rgb(0,0,0)"><font size="1">Post-doctoral researcher</font></div>
<div style="font-weight:normal; color:rgb(0,0,0)"><font size="1">Vision Lab, Dept. of Physics</font></div>
<div style="font-weight:normal; color:rgb(0,0,0)"><font size="1">University of Antwerp</font></div>
<div><font size="1">Universiteitsplein 1, N.1.18</font></div>
<div style="font-weight:normal; color:rgb(0,0,0)"><font size="1">B-2610 Wilrijk, Belgium</font></div>
<div><font size="1">Phone: +32 3 265 24 77</font></div>
<div style="font-weight:normal; color:rgb(0,0,0)"><font size="1">Email: ben.jeurissen@ua.ac.be</font></div>
<div style="font-weight:normal; color:rgb(0,0,0)"><font size="1">Url: <a href="http://visielab.ua.ac.be/people/ben-jeurissen" target="_blank">http://visielab.ua.ac.be/people/ben-jeurissen</a></font></div>
</div>
</div>
</div>
</div>
</div>
<div style="font-family: Times New Roman; color: #000000; font-size: 16px">
<hr tabindex="-1">
<div id="divRpF304579" style="direction: ltr;"><font face="Tahoma" size="2" color="#000000"><b>From:</b> mrtrix-discussion-bounces@public.nitrc.org [mrtrix-discussion-bounces@public.nitrc.org] on behalf of Alistair Perry [alistairperry123@gmail.com]<br>
<b>Sent:</b> 15 April 2013 04:34<br>
<b>To:</b> mrtrix-discussion@public.nitrc.org<br>
<b>Subject:</b> [Mrtrix-discussion] Gradient tables and csdeconv error<br>
</font><br>
</div>
<div></div>
<div>
<div dir="ltr">Dear Donald & Team,
<div><br>
</div>
<div>Let me introduce myself. My name is Alistair Perry and I am a post-graduate student at UNSW. Additionally Michael Breakspear at QIMR is my co-supervisor, so I will be using their pipeline, and I will meet you guys later in May.</div>
<div><br>
</div>
<div>I know this has been covered in previous posts, but this is an amalgamation of issues.</div>
<div><br>
</div>
<div>First, we have collected data in par/rec format from a 3T phillips scanner (b/vals = 1000, 31 directional). As obviously the gradient coordinates are not in mrtrix space and no DICOM format available, I had to flip the X-coordinates to achieve the desired
result. I have attached the formatted encoding file. Could you confirm this is the correct for MRtrix?</div>
<div><br>
</div>
<div>However, in doing so, and running csdeconv, I receive a number of error messages:
<b>csdeconv failed to converge</b> (I guess around +100 times). I have checked the resulting CSD orientation plot and everything appears to be ok, as does the resulting probalistic fiber tracks. There doesn't appear to be any voxels blacked out, although we
are using elderly subjects with obvious cortical atrophy. <br>
<br>
Suprisingly, when testing different iterations of the encoding file (i.e flipping Y or Z coordinates) this error did not appear. Could you explain why this is so? Is there a frequency of messages where it becomes a concern?</div>
<div><br>
</div>
<div>Thanks,</div>
<div><br>
</div>
<div>Alistair Perry</div>
</div>
</div>
</div>
</div>
</body>
</html>