Sure. Thank you!<br><br>best wishes,<br>Rali<br><br><div class="gmail_quote">On 26 March 2013 12:17, Matthew Webster <span dir="ltr">&lt;<a href="mailto:[log in to unmask]" target="_blank"><a href="/cgi-bin/wa-jisc.exe?LOGON=A3%3Dind1303%26L%3DFSL%26E%3Dquoted-printable%26P%3D5285660%26B%3D--047d7b343a9e187f8504d8ea48cb%26T%3Dtext%252Fhtml%3B%2520charset%3DISO-8859-1%26pending%3D" target="_parent" >[log in to unmask]</a></a>&gt;</span> wrote:<br>

<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div style="word-wrap:break-word"><div>Hello Rali,</div><div>                   I think the creators of the atlas are best equipped to answer which atlas is more appropriate, the link:</div>

<div><br></div><div><a href="http://cmrm.med.jhmi.edu" target="_blank">http://cmrm.med.jhmi.edu</a></div><div><br></div><div>should take you to pages with more information/contact details etc.</div><div><br></div><div>Kind Regards</div>

<span><font color="#888888"><div><br></div></font></span><div><span><font color="#888888">Matthew</font></span><div><div><br><blockquote type="cite">Hi<br><br>What I was actually wondering was which image (if any different)  is more appropriate for deriving a ROI skeleton mask.<br>

<br>Thank you.<br><br>Best wishes,<br>Rali<br><br><div class="gmail_quote">On 25 March 2013 10:07, Matthew Webster <span dir="ltr">&lt;<a href="mailto:[log in to unmask]" target="_blank"><a href="/cgi-bin/wa-jisc.exe?LOGON=A3%3Dind1303%26L%3DFSL%26E%3Dquoted-printable%26P%3D5285660%26B%3D--047d7b343a9e187f8504d8ea48cb%26T%3Dtext%252Fhtml%3B%2520charset%3DISO-8859-1%26pending%3D" target="_parent" >[log in to unmask]</a></a>&gt;</span> wrote:<br>


<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Dear Rali,<br>
                  JHU-WhiteMatter-labels-1mm.nii.gz is the summary image corresponding to the labels in JHU-labels.xml, JHU-ICBM-tracts-maxprob-thr0-1mm.nii.gz is a thresholded summary image from JHU-ICBM-tracts-prob-1mm.nii.gz and corresponds to the labels in JHU-tracts.xml.<br>



<br>
Kind Regards<br>
<span><font color="#888888"><br>
Matthew<br>
</font></span><div><div><br>
&gt; Dear all<br>
&gt;<br>
&gt; I am interested in performing TBSS ROI. The answers I found on the mailing list have been rather confusing and I was hoping that you could confirm that what I have decided to run is indeed appropriate.<br>
&gt;<br>
&gt; I have used the following command to define the SLF (L &amp; R):<br>
&gt;<br>
&gt; $FSLDIR/fslmaths  $FSLPATH/JHU-WhiteMatter-labels-1mm.nii.gz -thr $1 -uthr $2 -mas $MASKPATH/mean_FA_skeleton_mask  mask_SLF<br>
&gt;<br>
&gt; where $1 and $2 are the index taken from the JHU-labels.xml. The skeleton mask does correctly cover the ROI when displayed in fslview and the TBSS ROI results seem plausible considering initial whole-skeleton analyses. However I am confused to whether I should use the JHU-WhiteMatter-labels-1mm.nii.gz or the JHU-ICBM-tracts-maxprob-thr0-1mm.nii.gz . What is the difference?<br>



&gt;<br>
&gt; Thank you.<br>
&gt;<br>
&gt; Best wishes,<br>
&gt; Rali<br>
&gt;<br>
</div></div></blockquote></div><br><br clear="all"><br>-- <br><div>Best wishes,</div>
<div>Rali Dimitrova</div>
<div> </div>
<div>Division of Psychiatry,</div>
<div>University of Edinburgh </div>
</blockquote></div></div></div><br></div></blockquote></div><br><br clear="all"><br>-- <br><div>Best wishes,</div>
<div>Rali Dimitrova</div>
<div> </div>
<div>Division of Psychiatry,</div>
<div>University of Edinburgh </div>