<html dir="ltr">
<head>
<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1">
<style type="text/css" id="owaParaStyle"></style><style type="text/css"></style>
</head>
<body bgcolor="#FFFFFF" fpstyle="1" ocsi="0">
<div style="direction: ltr;font-family: Tahoma;color: #000000;font-size: 10pt;">Hi Romain,
<div><br>
</div>
<div>We are working on this. We hope to include it in one of the future releases.</div>
<div><br>
</div>
<div>For now, you can process the data by just using the outer shell:</div>
<div><br>
</div>
<div>1. Extract a single shell using the mrconvert command:</div>
<div><br>
</div>
<div>mrconvert -coord 3 idx1,idx2,... dwi.nii dwib03000.nii</div>
<div><br>
</div>
<div>Where idx1,idx2,... is a long list of indices of the b=0 and b=3000 images (indices starting from 0)</div>
<div>Extract the corresponding gradients from your gradient text file and save them in a new txt file.</div>
<div><br>
</div>
<div>2. Perform CSD and tracking as before with <span style="font-size: 10pt;">dwib3000.nii and the reduced grad file.</span></div>
<div><br>
</div>
<div>Cheers,</div>
<div>Ben</div>
<div>-</div>
<div>
<div>
<div>
<div style="widows: 2; orphans: 2;">
<div><font size="1"></font></div>
<font size="1">Ben Jeurissen, Ph.D.</font></div>
<div style="widows: 2; orphans: 2;">
<div><font size="1">Post-doctoral researcher</font></div>
<div><font size="1">Vision Lab, Dept. of Physics</font></div>
<div><font size="1">University of Antwerp</font></div>
<div><font size="1">Universiteitsplein 1, N.1.18</font></div>
<div><font size="1">B-2610 Wilrijk, Belgium</font></div>
<div><font size="1">Phone: +32 3 265 24 77</font></div>
<div><font size="1">Email: ben.jeurissen@ua.ac.be</font></div>
<div><font size="1">Url: <a title="http://visielab.ua.ac.be/people/ben-jeurissen
Ctrl+Click to follow link" 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><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 title="http://visielab.ua.ac.be/people/ben-jeurissen
Ctrl+Click to follow link" 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="divRpF577846" 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 romain valabregue [romain.valabregue@upmc.fr]<br>
<b>Sent:</b> 03 July 2013 14:49<br>
<b>To:</b> mrtrix-discussion@public.nitrc.org<br>
<b>Subject:</b> Re: [Mrtrix-discussion] multiple bvalue<br>
</font><br>
</div>
<div></div>
<div>
<div class="moz-cite-prefix">Dear all<br>
<br>
Summer is there (and vacations are coming) so it may not be the perfect time to put it forward. But just in case ...<br>
<br>
Since I am playin with the very nice connectome data I can not stop thinking : it would be great to have a multi shell version of the odf within mrtrix.<br>
<br>
Have a look at connectome data It may give you the motivation ... 288 direction (with 3 shell 1000 2000 3000) 1.25 isotropic resolution perfect corregistration with a T1 0.7iso volume, 40 subject easy to dowload.
<br>
It is worth to try !<br>
<br>
All the best<br>
<br>
Romain<br>
<br>
<br>
<br>
<br>
Le 16/11/2012 02:31, Donald Tournier a écrit :<br>
</div>
<blockquote type="cite">Hi everyone,
<div><br>
</div>
<div>The DTI fit in MRtrix should handle multiple b-values fine. The CSD approach however cannot currently handle such data, as Thijs correctly stated. Luis, I'm surprised that you manage to get convincing results simply by stripping off the b=0 image, since
it is ignored by csdeconv anyway (unless you use the -normalise option which is not recommended). In any case, it is definitely not designed to handle multiple b-values, so I would not advise planning your study around it...</div>
<div><br>
</div>
<div>Cheers,</div>
<div><br>
</div>
<div>Donald.</div>
<div><br>
</div>
<div><br>
<div class="gmail_quote">On 16 November 2012 07:41, Luis Concha <span dir="ltr"><<a href="mailto:lconcha@unam.mx" target="_blank">lconcha@unam.mx</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0
.8ex; border-left:1px #ccc solid; padding-left:1ex">
I have a similar data set to the one described by Romain (1x b=0, 32x b=1000 and 32x b=2000; the 32 gradient directions are identical for b1000 and b2000).
<br>
<br>
Perhaps I _shouldn't_ be doing it, but cdsdeconv seems to handle this data set perfectly when I strip off the b=0 image (my usual approach, as I am after CSF signal elimination). However, I just tested csdeconv with all three b values (0,1000 and 2000) and
it seems to give similar results, up to an lmax=6 (I did not test any further).<br>
<br>
The DTI maps look perfectly fine, with a slight increase in FA in regions partial voluming with CSF (fornix, callosum edges) in the non-b0 data set as compared to the b=0,1000,2000 data set.<br>
<br>
Perhaps doing 2 shells is OK even in the absence of b=0, and the argument of multi-shell CSD invalidity is only applicable for >3 shells. Nonetheless, I would much appreciate it if you could direct me to the right papers in order to understand if I am doing
things properly, as I plan to use this approach for a longitudinal 4-year study that is just about to begin.<br>
<br>
Below is the gradient table used for the b=0,1000,2000 data set, and I am posting a snapshot of the orientation plots for the data sets I mentioned here:<br>
<a href="http://imgur.com/56Y8q" target="_blank">http://imgur.com/56Y8q</a><br>
<br>
<br>
Thanks.<br>
<br>
<br clear="all">
Dr. Luis Concha<br>
Instituto de Neurobiología<br>
Laboratorio C-12<br>
UNAM, Campus Juriquilla<br>
Boulervard Juriquilla 3001<br>
Juriquilla, Querétaro.<br>
C.P. 76230<br>
México<br>
Tel <a href="tel:%28442%29%202%2038%2010%2053" value="+524422381053" target="_blank">
(442) 2 38 10 53</a><br>
Fax <a href="tel:%28442%29%202%2038%2010%2046" value="+524422381046" target="_blank">
(442) 2 38 10 46</a><br>
<a href="http://www.inb.unam.mx" target="_blank">www.inb.unam.mx</a><br>
<br>
0.000000 0.000000 0.000000 0<br>
-1.000000 0.000000 0.000000 1000<br>
0.000000 -1.000000 0.000000 1000<br>
0.000000 0.000000 1.000000 1000<br>
0.042400 0.114601 -0.992506 1000<br>
-0.174909 0.200511 -0.963951 1000<br>
-0.232290 0.162593 -0.958960 1000<br>
-0.367520 -0.026101 -0.929649 1000<br>
-0.190192 -0.374383 -0.907560 1000<br>
0.116799 -0.833394 -0.540196 1000<br>
0.200489 -0.252686 -0.946548 1000<br>
0.495782 -0.134495 -0.857969 1000<br>
0.014100 0.628102 -0.778003 1000<br>
0.744490 0.147698 -0.651091 1000<br>
0.760877 -0.320390 -0.564283 1000<br>
0.180892 -0.924660 -0.335085 1000<br>
0.679628 0.422417 -0.599725 1000<br>
-0.777100 -0.470700 -0.417800 1000<br>
-0.924162 0.103596 -0.367685 1000<br>
-0.468485 0.767376 -0.437786 1000<br>
-0.881688 0.189298 -0.432194 1000<br>
-0.690404 -0.706204 -0.156901 1000<br>
-0.239096 -0.757087 -0.607990 1000<br>
0.057800 -0.983696 0.170299 1000<br>
0.536773 -0.836058 -0.113494 1000<br>
0.991788 0.120698 -0.042299 1000<br>
0.996763 -0.070897 -<a href="tel:0.037899%C2%A0%C2%A0%C2%A0%201000" value="+3780549991000" target="_blank">0.037899 1000</a><br>
0.872425 -0.478114 -0.101403 1000<br>
0.248714 -0.933552 0.258114 1000<br>
-0.118295 -0.991861 -0.047098 1000<br>
-0.337598 -0.841495 0.421798 1000<br>
-0.528585 -0.840876 0.116297 1000<br>
-0.996853 -0.054997 -0.057097 1000<br>
-1.000000 0.000000 0.000000 2000<br>
0.000000 -1.000000 0.000000 2000<br>
0.000000 0.000000 1.000000 2000<br>
0.042400 0.114601 -0.992506 2000<br>
-0.174909 0.200511 -0.963951 2000<br>
-0.232290 0.162593 -0.958960 2000<br>
-0.367520 -0.026101 -0.929649 2000<br>
-0.190192 -0.374383 -0.907560 2000<br>
0.116799 -0.833394 -0.540196 2000<br>
0.200489 -0.252686 -0.946548 2000<br>
0.495782 -0.134495 -0.857969 2000<br>
0.014100 0.628102 -0.778003 2000<br>
0.744490 0.147698 -0.651091 2000<br>
0.760877 -0.320390 -0.564283 2000<br>
0.180892 -0.924660 -0.335085 2000<br>
0.679628 0.422417 -0.599725 2000<br>
-0.777100 -0.470700 -0.417800 2000<br>
-0.924162 0.103596 -0.367685 2000<br>
-0.468485 0.767376 -0.437786 2000<br>
-0.881688 0.189298 -0.432194 2000<br>
-0.690404 -0.706204 -0.156901 2000<br>
-0.239096 -0.757087 -0.607990 2000<br>
0.057800 -0.983696 0.170299 2000<br>
0.536773 -0.836058 -0.113494 2000<br>
0.991788 0.120698 -0.042299 2000<br>
0.996763 -0.070897 -<a href="tel:0.037899%C2%A0%C2%A0%C2%A0%202000" value="+3780549992000" target="_blank">0.037899 2000</a><br>
0.872425 -0.478114 -0.101403 2000<br>
0.248714 -0.933552 0.258114 2000<br>
-0.118295 -0.991861 -0.047098 2000<br>
-0.337598 -0.841495 0.421798 2000<br>
-0.528585 -0.840876 0.116297 2000<br>
-0.996853 -0.054997 -0.057097 2000<br>
<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>
<br>
</div>
<br>
<fieldset class="mimeAttachmentHeader" target="_blank"></fieldset> <br>
<pre>_______________________________________________
Mrtrix-discussion mailing list
<a class="moz-txt-link-abbreviated" href="mailto:Mrtrix-discussion@www.nitrc.org" target="_blank">Mrtrix-discussion@www.nitrc.org</a>
<a class="moz-txt-link-freetext" href="http://www.nitrc.org/mailman/listinfo/mrtrix-discussion" target="_blank">http://www.nitrc.org/mailman/listinfo/mrtrix-discussion</a>
</pre>
</blockquote>
<br>
</div>
</div>
</div>
</body>
</html>