<div dir="ltr"><div><div><div><div>Romain<br><br></div>There is a class in the code back-end that receives the diffusion weighting gradient table, and attempts to <i>cluster</i> the b-values into discrete shells.<br>It does so in a way that allows for some level of variance in the actual b-values as reported by the gradient table (such as that you have provided), so that even if the b-values are not precisely identical, they will still be grouped into the same shell.<br>
</div>When this process is completed, each b-value shell is characterised internally by the mean / stdev / minimum / maximum b-value in the shell. When you provide a 'desired' b-value using the <span style="font-family:courier new,monospace">-shell</span> option, this value is compared to the shell classification as produced by the clustering algorithm, such that you don't have to specify precisely the mean b-value at the command-line in order to select the shell you want. If however there are multiple shells in your data, and your b-value request cannot be unambiguously assigned to one of those shells (e.g. the data has b=0,1000,2000,3000 shells and you specify <span style="font-family:courier new,monospace">-shell 2500</span>) the command should give you an error.<br>
</div><div>Also note that if you try to feed a DSI acquisition to such a command, the clustering algorithm <i>should</i> also identify the fact that a shell-like classification is not appropriate for these data, and provide an error message accordingly.<br>
</div><div><br></div>Regarding the use of multiple shells: We now have a neat command construction framework that allows a standardised command-line option to be accessed in multiple commands (so we don't have to repeatedly duplicate them). This is used to define the <span style="font-family:courier new,monospace">-shell</span> option for all commands that make use of it, and all of those commands construct the class described above for the b-value clustering. Since there is at least one command (<span style="font-family:courier new,monospace">dwiextract</span> from memory) that allows the use of multiple b-value shells, the command-line option states 'one or more'. However you should find that if you provide more than one b-value to a command such as <span style="font-family:courier new,monospace">dwi2fod</span> (e.g. <span style="font-family:courier new,monospace">-shell 1000,2000,3000</span>), it should give you an appropriate error message.<br>
<br></div>Best regards<br>Rob<br></div><div class="gmail_extra"><br clear="all"><div><div dir="ltr"><br>--<br><br><span style="color:rgb(255,102,0)"><b>Robert Smith, Ph.D</b><br>Research Officer, Imaging Division</span><br>
<br>The Florey Institute of Neuroscience and Mental Health<br>Melbourne Brain Centre - Austin Campus<br>245 Burgundy Street<br>Heidelberg Vic 3084<br>Ph: +61 3 9035 7128<br>Fax: +61 3 9035 7301<br><a href="http://www.florey.edu.au" target="_blank">www.florey.edu.au</a><br>
<span style="font-size:9pt;font-family:"Times New Roman","serif";color:red"></span></div></div>
<br><br><div class="gmail_quote">On Wed, May 21, 2014 at 5:37 PM, romain valabregue <span dir="ltr"><<a href="mailto:romain.valabregue@upmc.fr" target="_blank">romain.valabregue@upmc.fr</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div bgcolor="#FFFFFF" text="#000000">
<div>Hi Robert<br>
<br>
Thanks for the clarification. Just one more precision then<br>
what happend if I have a list a bvalue like<br>
<br>
0 0 0 3005 2995 3000 2990 2995 3010 3005 2985 3005 2990 300<br>
<br>
It should not be consider as a multishell. What is then the range
you consider as being the same b value ?<br>
<br>
<br>
<br>
Note that the documentation :<br>
-shell list<br>
specify one or more diffusion-weighted gradient shells to use
during<br>
processing ...<br>
<br>
this suggest that you can take into account more than one
diffusion shells ...<br>
<br>
<br>
romain<br>
<br>
<br>
<br>
Le 21/05/2014 09:10, Robert Smith a écrit :<br>
</div><div><div class="h5">
<blockquote type="cite">
<div dir="ltr">Hi Romain<br>
<ol>
<li>The previous functionality of <span style="font-family:courier new,monospace">filter_tracks</span>
can now be found in the <span style="font-family:courier new,monospace">tckedit</span> command. This command is a
bit of a track-editing workhorse; check the -help page to
see all of its functionality.</li>
<li>We currently do not have genuine multi-shell processing,
though we hope to introduce it in the future. The -shell
option in <span style="font-family:courier new,monospace">dwi2fod</span>
(the same option also exists in other dwi-related commands)
simply specifies the b-value in a multi-shell acquisition to
be extracted for use in subsequent processing. If a
multi-shell acquisition is received as input, and the -shell
option is <i>not</i> provided, the command will extract and
use only the highest b-value shell by default.</li>
</ol>
<p>Cheers</p>
<p>Rob<br>
</p>
</div>
<div class="gmail_extra"><br clear="all">
<div>
<div dir="ltr"><br>
--<br>
<br>
<span style="color:rgb(255,102,0)"><b>Robert Smith, Ph.D</b><br>
Research Officer, Imaging Division</span><br>
<br>
The Florey Institute of Neuroscience and Mental Health<br>
Melbourne Brain Centre - Austin Campus<br>
245 Burgundy Street<br>
Heidelberg Vic 3084<br>
Ph: <a href="tel:%2B61%203%209035%207128" value="+61390357128" target="_blank">+61 3 9035 7128</a><br>
Fax: <a href="tel:%2B61%203%209035%207301" value="+61390357301" target="_blank">+61 3 9035 7301</a><br>
<a href="http://www.florey.edu.au/" target="_blank">www.florey.edu.au</a><br>
</div>
</div>
<br>
<br>
<div class="gmail_quote">On Wed, May 21, 2014 at 6:25 AM, romain
valabregue <span dir="ltr"><<a href="mailto:romain.valabregue@upmc.fr" target="_blank">romain.valabregue@upmc.fr</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Hello<br>
<br>
Two short questions about the very nice new version (I just
started to test)<br>
<br>
1_ I did not find the equivalent of the previous function
filter_tracks<br>
<br>
2_ In the dwi2fod function I do not understand the -sehlll
options. Can I use it with a multishell dataset not already
? (the bvalue are already in the gradient table)<br>
<br>
<br>
Many thanks (and congratulation for the nice viewer)<br>
<br>
Romain<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>
</blockquote>
</div>
<br>
</div>
</blockquote>
<br>
</div></div></div>
<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></div>