Dear Anderson,<div><br></div><div>what does it mean to make executable and therefore be able to omit the sh?</div><div><br></div><div>thanks a lot</div><div><br></div><div>cheers,</div><div>sandra<br><br><div class="gmail_quote">
2013/2/14 Anderson M. Winkler <span dir="ltr">&lt;<a href="mailto:[log in to unmask]" target="_blank"><a href="/cgi-bin/wa-jisc.exe?LOGON=A3%3Dind1302%26L%3DFSL%26E%3Dquoted-printable%26P%3D4622576%26B%3D--f46d04389251a6eab504d5b5a5b4%26T%3Dtext%252Fhtml%3B%2520charset%3DISO-8859-1%26pending%3D" target="_parent" >[log in to unmask]</a></a>&gt;</span><br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div dir="ltr">Dear Bonnie and Mingxia,<br>Yep, that&#39;s right. And if the &quot;autoaq&quot; is made executable, the &quot;sh&quot; at the beginning can be omitted.<br>Note that the &quot;autoaq&quot; isn&#39;t a replacement for &quot;atlasquery&quot;, but just an interface to it. Both &quot;atlasquery&quot; and &quot;cluster&quot; are used behind the scenes.<br>



All the best,<br>Anderson<br></div><div class="HOEnZb"><div class="h5"><div class="gmail_extra"><br><br><div class="gmail_quote">2013/2/14 zhang mingxia <span dir="ltr">&lt;<a href="mailto:[log in to unmask]" target="_blank"><a href="/cgi-bin/wa-jisc.exe?LOGON=A3%3Dind1302%26L%3DFSL%26E%3Dquoted-printable%26P%3D4622576%26B%3D--f46d04389251a6eab504d5b5a5b4%26T%3Dtext%252Fhtml%3B%2520charset%3DISO-8859-1%26pending%3D" target="_parent" >[log in to unmask]</a></a>&gt;</span><br>


<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">Hi Bonnie,<div><br></div><div>I put it in a directory and then go into that directory. Suppose you want to know the name of the cluster in your x.nii.gz file based on &quot; Harvard-Oxford Cortical Structural Atlas&quot; with the threshold p&gt;.95. Use the code like this:</div>



<div><br></div><div>sh ./<span style="font-family:&#39;Courier New&#39;;font-size:16.000003814697266px">autoaq -i x.nii.gz -a &quot;</span>Harvard-Oxford Cortical Structural Atlas&quot; -t .95 -o try.txt</div>
<div><br></div><div>Open the try.txt and you will know what&#39;s this script for. I think this one is an improvement of <a href="http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/Atlasquery" target="_blank">http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/Atlasquery</a>.</div>



<div><br></div><div>You should notice there are special names for atlas, you can only use these:</div><div><br></div><div><div>Cerebellar Atlas in MNI152 space after normalization with FLIRT</div><div>
Cerebellar Atlas in MNI152 space after normalization with FNIRT</div><div>Harvard-Oxford Cortical Structural Atlas</div><div>Harvard-Oxford Subcortical Structural Atlas</div><div>JHU ICBM-DTI-81 White-Matter Labels</div>


<div>
JHU White-Matter Tractography Atlas</div><div>Juelich Histological Atlas</div><div>MNI Structural Atlas</div><div>Oxford Thalamic Connectivity Probability Atlas</div><div>Oxford-Imanova Striatal Connectivity Atlas 3 sub-regions</div>



<div>Oxford-Imanova Striatal Connectivity Atlas 7 sub-regions</div><div>Oxford-Imanova Striatal Structural Atlas</div><div>Subthalamic Nucleus Atlas</div><div>Talairach Daemon Labels</div><div><br></div></div><div><br>
</div><div>Please let me know if you have any other questions.</div><span><font color="#888888"><div><br></div><div>Mingxia</div></font></span></div><div><div><div class="gmail_extra">

<br><br><div class="gmail_quote">On Thu, Feb 14, 2013 at 4:10 AM, Bonnie Lam <span dir="ltr">&lt;<a href="mailto:[log in to unmask]" target="_blank"><a href="/cgi-bin/wa-jisc.exe?LOGON=A3%3Dind1302%26L%3DFSL%26E%3Dquoted-printable%26P%3D4622576%26B%3D--f46d04389251a6eab504d5b5a5b4%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><div style="font-size:12pt;font-family:times new roman,new york,times,serif"><div>Hi Mingxia,</div><div><br></div>



<div>Thanks for your reply. </div><div><br></div><div>Would you mind further explaining how to use the script?</div><div><br></div><div>So I assume you will first need to replace your files in the brackets: <p><span style="font-family:&#39;Courier New&#39;">autoaq -i &lt;input image&gt; -a &quot;&lt;atlas name&gt;&quot; -t &lt;threshold&gt; -o &lt;output.txt&gt;<br>



 <br> </span></p><p><span style="font-family:&#39;Courier New&#39;"><span style="font-family:&#39;times new roman&#39;,&#39;new york&#39;,times,serif">And also add your files here :</span> <span style="font-family:&#39;times new roman&#39;,&#39;new york&#39;,times,serif"></span></span></p>



<p><span style="font-family:&#39;Courier New&#39;"></span></p><p><span style="font-family:&#39;Courier New&#39;">IN=&quot;&quot;<br> ATLAS=&quot;&quot;<br> OUT=&quot;&quot;<br> </span></p><p><span style="font-family:&#39;times new roman&#39;,&#39;new york&#39;,times,serif"><span face="Courier New" style="font-family:&#39;Courier New&#39;"><span style="font-family:&#39;times new roman&#39;,&#39;new york&#39;,times,serif">Then in your working directory, type in: sh autoaq.sh ?</span><br>



</span></span></p><p><span style="font-family:&#39;times new roman&#39;,&#39;new york&#39;,times,serif">Thanks for your reply in advance!</span></p><p><span style="font-family:&#39;times new roman&#39;,&#39;new york&#39;,times,serif">Cheers,</span></p>



<p><span style="font-family:&#39;times new roman&#39;,&#39;new york&#39;,times,serif">Bonnie</span></p><p><span style="font-family:&#39;Courier New&#39;"><br></span></p></div><div><br></div><hr><div style="font-size:12pt;font-style:normal;font-family:Helvetica,Arial,sans-serif;text-decoration:none;font-weight:normal">



<b>From: </b>&quot;zhang mingxia&quot; &lt;<a href="mailto:[log in to unmask]" target="_blank"><a href="/cgi-bin/wa-jisc.exe?LOGON=A3%3Dind1302%26L%3DFSL%26E%3Dquoted-printable%26P%3D4622576%26B%3D--f46d04389251a6eab504d5b5a5b4%26T%3Dtext%252Fhtml%3B%2520charset%3DISO-8859-1%26pending%3D" target="_parent" >[log in to unmask]</a></a>&gt;<br><b>To: </b><a href="mailto:[log in to unmask]" target="_blank"><a href="/cgi-bin/wa-jisc.exe?LOGON=A3%3Dind1302%26L%3DFSL%26E%3Dquoted-printable%26P%3D4622576%26B%3D--f46d04389251a6eab504d5b5a5b4%26T%3Dtext%252Fhtml%3B%2520charset%3DISO-8859-1%26pending%3D" target="_parent" >[log in to unmask]</a></a><br>



<b>Sent: </b>Thursday, February 14, 2013 8:42:59 PM<br><b>Subject: </b>Re: [FSL] Reporting p-value, cluster size and percentage of tract involved all in one<div><div><br><div><br></div><div dir="ltr">Here is a script. Please see the one mail in the mail list today about the atlasquesry.</div>



<div class="gmail_extra"><br><div><br></div><div class="gmail_quote">On Wed, Feb 13, 2013 at 9:09 PM, Bonnie Y K Lam <span dir="ltr">&lt;<a href="mailto:[log in to unmask]" target="_blank"><a href="/cgi-bin/wa-jisc.exe?LOGON=A3%3Dind1302%26L%3DFSL%26E%3Dquoted-printable%26P%3D4622576%26B%3D--f46d04389251a6eab504d5b5a5b4%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 FSL users,<br> <br> I have been following post from other FSL users in regards to using the cluster and altasquery command. However, the question remains as to whether there is a way to report p-value, cluster size and tract info in the same txt file?<br>



 <br> In the cluster command we can get the cluster size, t-value, MNI coordinates, etc and output as follow:<br> <br> Cluster Index   Voxels  MAX     MAX X (mm)      MAX Y (mm)      MAX Z (mm)      COG X (mm)      COG Y (mm)      COG Z (mm)<br>



 2       1106    0.961   6       4       24      -1.01   -4.29   25.6<br> 1       28      0.951   -6      -35     20      -8.18   -34.4   21.4<br> <br> <br> And in the atlasquery command we get the tract and percentage involved (in the case, the JHU White-Matter atlas is used)<br>



 <br> Anterior thalamic radiation L:1.18646<br> Anterior thalamic radiation R:1.01869<br> Corticospinal tract L:<a href="tel:0.759451" value="+390759451" target="_blank">0.759451</a><br> Corticospinal tract R:<a href="tel:0.373157" value="+390373157" target="_blank">0.373157</a><br>
 Cingulum (cingulate gyrus) L:<a href="tel:0.259725" value="+390259725" target="_blank">0.259725</a><br> Cingulum (cingulate gyrus) R:<a href="tel:0.104708" value="+390104708" target="_blank">0.104708</a><br>


 Cingulum (hippocampus) L:0.0153588<br> Cingulum (hippocampus) R:0.0297155<br> Forceps major:1.02095<br> Forceps minor:2.68633<br> Inferior fronto-occipital fasciculus L:1.72625<br> Inferior fronto-occipital fasciculus R:1.5613<br>



 Inferior longitudinal fasciculus L:1.51863<br> Inferior longitudinal fasciculus R:<a href="tel:0.703462" value="+390703462" target="_blank">0.703462</a><br> Superior longitudinal fasciculus L:2.59552<br> Superior longitudinal fasciculus R:1.42251<br>
 Uncinate fasciculus L:<a href="tel:0.566331" value="+390566331" target="_blank">0.566331</a><br>


 Uncinate fasciculus R:<a href="tel:0.211678" value="+390211678" target="_blank">0.211678</a><br> Superior longitudinal fasciculus (temporal part) L:1.14275<br> Superior longitudinal fasciculus (temporal part) R:<a href="tel:0.46396" value="+39046396" target="_blank">0.46396</a><br>
 <br> If I would like to report on<br> <br> Tract name, percentage involved, cluster size and p-value PER TRACT<br>


 <br> what would be the best way to do it?<br> <br> Thank you very much,<br> <br> Bonnie<br></blockquote></div><br></div></div></div></div><span><font color="#888888"><div><br><br></div><div><br></div><div>
-- <br></div><div><span name="x"></span><div style="font-size:medium"><p style="font-size:12px;font-family:arial,verdana,helvetica,sans-serif;font-weight:bold">Bonnie Yin Ka Lam<br>PhD Candidate</p></div><div style="font-size:medium">



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PO Box 1165 Randwick Sydney NSW 2031 Australia<br><b>T</b> <a href="tel:%2B61%202%209399%201803" value="+61293991803" target="_blank">+61 2 9399 1803</a></p></div><span name="x"></span><br></div></font></span></div></div>



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