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">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>