Hi David,<div><br><div><div>Thanks for your reply.</div><div><br></div><div>I still have problem. </div><div><br></div><div>I have run thresholding on my aal-prob-2mm.nii and now I have these files in the same directory:</div>
<div>aal-maxprob-thr0-2mm.nii.gz</div><div>aal-maxprob-thr25-2mm.nii.gz</div><div>aal-maxprob-thr50-2mm.nii.gz</div></div><div><br></div><div> and I have corrected xml in this way:</div><div><br></div><div><p style="margin: 0.0px 0.0px 0.0px 0.0px; font: 11.0px Menlo; color: #9533b8">
<span style="color: #b72612">&lt;?xml</span><span style="color: #000000"> </span><span style="color: #3f8c97">version</span><span style="color: #000000">=</span>&quot;1.0&quot;<span style="color: #000000"> </span><span style="color: #3f8c97">encoding</span><span style="color: #000000">=</span>&quot;ISO-8859-1&quot;<span style="color: #000000">?</span><span style="color: #b72612">&gt;</span></p>

<p style="margin: 0.0px 0.0px 0.0px 0.0px; font: 11.0px Menlo"><span style="color: #b72612">&lt;</span>atlas <span style="color: #3f8c97">version</span>=<span style="color: #9533b8">&quot;1.0&quot;</span><span style="color: #b72612">&gt;</span></p>

<p style="margin: 0.0px 0.0px 0.0px 0.0px; font: 11.0px Menlo">  <span style="color: #b72612">&lt;</span>header<span style="color: #b72612">&gt;</span></p>
<p style="margin: 0.0px 0.0px 0.0px 0.0px; font: 11.0px Menlo">    <span style="color: #b72612">&lt;</span>name<span style="color: #b72612">&gt;</span>MRIcro <span style="color: #1738f5">222</span> Atlas<span style="color: #b72612">&lt;/</span>name<span style="color: #b72612">&gt;</span></p>

<p style="margin: 0.0px 0.0px 0.0px 0.0px; font: 11.0px Menlo">    <span style="color: #b72612">&lt;</span>type<span style="color: #b72612">&gt;</span>Label<span style="color: #b72612">&lt;/</span>type<span style="color: #b72612">&gt;</span></p>

<p style="margin: 0.0px 0.0px 0.0px 0.0px; font: 11.0px Menlo">    <span style="color: #b72612">&lt;</span>images<span style="color: #b72612">&gt;</span></p>
<p style="margin: 0.0px 0.0px 0.0px 0.0px; font: 11.0px Menlo">    <span style="color: #b72612">&lt;</span>imagefile<span style="color: #b72612">&gt;</span>/aai/aal-prob-2mm<span style="color: #b72612">&lt;/</span>imagefile<span style="color: #b72612">&gt;</span></p>

<p style="margin: 0.0px 0.0px 0.0px 0.0px; font: 11.0px Menlo">      <span style="color: #b72612">&lt;</span>summaryimagefile<span style="color: #b72612">&gt;</span>/aai/aal-maxprob-thr25-2mm<span style="color: #b72612">&lt;/</span>summaryimagefile<span style="color: #b72612">&gt;</span></p>

<p style="margin: 0.0px 0.0px 0.0px 0.0px; font: 11.0px Menlo">    <span style="color: #b72612">&lt;/</span>images<span style="color: #b72612">&gt;</span></p>
<p style="margin: 0.0px 0.0px 0.0px 0.0px; font: 11.0px Menlo">  <span style="color: #b72612">&lt;/</span>header<span style="color: #b72612">&gt;</span></p>
<p style="margin: 0.0px 0.0px 0.0px 0.0px; font: 11.0px Menlo">  <span style="color: #b72612">&lt;</span>data<span style="color: #b72612">&gt;</span></p>
<p style="margin: 0.0px 0.0px 0.0px 0.0px; font: 11.0px Menlo"><span style="color: #b72612">&lt;</span>label index=<span style="color: #9533b8">&quot;1&quot;</span><span style="color: #b72612">&gt;</span> Precentral_L <span style="color: #1738f5">2001</span><span style="color: #b72612">&lt;/</span>label<span style="color: #b72612">&gt;</span> </p>

<p style="margin: 0.0px 0.0px 0.0px 0.0px; font: 11.0px Menlo"><span style="color: #b72612">&lt;</span>label index=<span style="color: #9533b8">&quot;2&quot;</span><span style="color: #b72612">&gt;</span> Precentral_R <span style="color: #1738f5">2002</span><span style="color: #b72612">&lt;/</span>label<span style="color: #b72612">&gt;</span></p>

<p style="margin: 0.0px 0.0px 0.0px 0.0px; font: 11.0px Menlo"><span style="color: #b72612">&lt;</span>label index=<span style="color: #9533b8">&quot;3&quot;</span><span style="color: #b72612">&gt;</span> Frontal_Sup_L <span style="color: #1738f5">2101</span><span style="color: #b72612">&lt;/</span>label<span style="color: #b72612">&gt;</span></p>

<p style="margin: 0.0px 0.0px 0.0px 0.0px; font: 11.0px Menlo"><span style="color: #b72612">&lt;</span>label index=<span style="color: #9533b8">&quot;4&quot;</span><span style="color: #b72612">&gt;</span> Frontal_Sup_R <span style="color: #1738f5">2102</span><span style="color: #b72612">&lt;/</span>label<span style="color: #b72612">&gt;</span></p>
<p style="margin: 0.0px 0.0px 0.0px 0.0px; font: 11.0px Menlo"><span style="color: #b72612"><br></span></p><p style="margin: 0.0px 0.0px 0.0px 0.0px; font: 11.0px Menlo"><span style="color: #b72612">.........</span></p><p style="margin: 0.0px 0.0px 0.0px 0.0px; font: 11.0px Menlo">
<span style="color: #b72612"><br></span></p><p style="margin: 0.0px 0.0px 0.0px 0.0px; font: 11.0px Menlo"><span style="color: #b72612"><br></span></p><p style="margin: 0.0px 0.0px 0.0px 0.0px; font: 11.0px Menlo"><span style="color: #b72612"><br>
</span></p><p style="margin: 0.0px 0.0px 0.0px 0.0px; font: 11.0px Menlo"><span style="color: #b72612"></span></p><p style="margin: 0.0px 0.0px 0.0px 0.0px; font: 11.0px Menlo"><span style="color: #b72612">&lt;</span>label index=<span style="color: #9533b8">&quot;115&quot;</span><span style="color: #b72612">&gt;</span> Vermis_<span style="color: #1738f5">9</span> <span style="color: #1738f5">9160</span><span style="color: #b72612">&lt;/</span>label<span style="color: #b72612">&gt;</span></p>

<p style="margin: 0.0px 0.0px 0.0px 0.0px; font: 11.0px Menlo"><span style="color: #b72612">&lt;</span>label index=<span style="color: #9533b8">&quot;116&quot;</span><span style="color: #b72612">&gt;</span> Vermis_<span style="color: #1738f5">10</span> <span style="color: #1738f5">9170</span><span style="color: #b72612">&lt;/</span>label<span style="color: #b72612">&gt;</span></p>

<p style="margin: 0.0px 0.0px 0.0px 0.0px; font: 11.0px Menlo">  <span style="color: #b72612">&lt;/</span>data<span style="color: #b72612">&gt;</span></p>
<p style="margin: 0.0px 0.0px 0.0px 0.0px; font: 11.0px Menlo"><span style="color: #b72612">&lt;/</span>atlas<span style="color: #b72612">&gt;</span></p><div><span style="color: #b72612"><br></span></div><div><span style="color: #b72612"><br>
</span></div><div><span style="color: #b72612"><br></span></div><div><span style="color: #b72612"><div>but aal atlas does not appear in  &quot;Atlas Selection&quot; windows.</div><div>I have looked a bit in archive and I have found this post:</div>
</span></div><p></p><p style="margin: 0.0px 0.0px 0.0px 0.0px; font: 11.0px Menlo"><span style="color: #b72612"><br></span></p></div><div><a href="https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0910&amp;L=FSL&amp;D=0&amp;1=FSL&amp;9=A&amp;I=-3&amp;J=on&amp;K=1&amp;X=20ABF201A81057049C&amp;Y=serenaf33%40gmail.com&amp;d=No+Match%3BMatch%3BMatches&amp;z=4&amp;P=221013">https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0910&amp;L=FSL&amp;D=0&amp;1=FSL&amp;9=A&amp;I=-3&amp;J=on&amp;K=1&amp;X=20ABF201A81057049C&amp;Y=serenaf33%40gmail.com&amp;d=No+Match%3BMatch%3BMatches&amp;z=4&amp;P=221013</a></div>
<div><br></div><div>I have MAC 10.6.4 (Snow Leopard) and I am using FSL 4.1.5 I have not older FSL version.  </div><div>Could the version of my MAC be the problem? </div><div><br></div><div>Thanks again for your help.</div>
<div><br></div><div>Serena.</div><div><br></div><div><br></div><div><br><div class="gmail_quote">On Mon, Oct 18, 2010 at 6:32 PM, David Flitney <span dir="ltr">&lt;<a href="mailto:[log in to unmask]"><a href="/cgi-bin/wa-jisc.exe?LOGON=A3%3Dind1010%26L%3DFSL%26E%3Dquoted-printable%26P%3D2059377%26B%3D--001485f629caf075a90492f94791%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">In your XML file: the &quot;imagefile&quot; and &quot;summaryimagefile&quot; nodes need to exist within an &quot;images&quot; section. Also you&#39;ve specified aal_2mm as both the image and it&#39;s own summary. Your image ought to be a 4D 116 volume float image where each volume is the probability of the corresponding region. The summary ought to be a 3D volume with 116 labels outlining the locations of the different regions. There is a script in $FSLDIR/data/atlases/bin called &quot;threshold&quot; which will do this for you although I notice it expects images to be named of the form aal-prob-2mm.nii.gz<div>
<br></div><div>Hope that helps,</div><div>Dave<div><br></div><div><div><div><div></div><div class="h5"><div>On 18 Oct 2010, at 15:39, sere f wrote:</div><br></div></div><blockquote type="cite"><div><div></div><div class="h5">
<br><br><div class="gmail_quote"><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div>On Mon, Oct 18, 2010 at 4:33 PM, sere f <span dir="ltr">&lt;<a href="mailto:[log in to unmask]" target="_blank"><a href="/cgi-bin/wa-jisc.exe?LOGON=A3%3Dind1010%26L%3DFSL%26E%3Dquoted-printable%26P%3D2059377%26B%3D--001485f629caf075a90492f94791%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-top:0px;margin-right:0px;margin-bottom:0px;margin-left:0.8ex;border-left-width:1px;border-left-color:rgb(204, 204, 204);border-left-style:solid;padding-left:1ex">
Hi David,<div>thanks for your prompt reply.</div><div><br></div><div>I don&#39;t understand where I have to write this line:</div><div><div>name &quot;Blah&quot; - from &lt;name&gt;Blah&lt;/name&gt;</div><div><br>
</div></div><div>Anyway:</div><div><br></div><div>aal.xml is in Attach and this is the output of    ls -lR $FSL/data/atlases:</div><div><br></div><div><br></div><div><div>total 360</div><div>drwxr-xr-x@ 18 fabbri  staff     612 Jan 26  2010 Cerebellum</div>

<div>-rwxr-xr-x@  1 fabbri  staff    2271 Feb 26  2009 Cerebellum_MNIflirt.xml</div><div>-rwxr-xr-x@  1 fabbri  staff    2271 Feb 26  2009 Cerebellum_MNIfnirt.xml</div><div>drwxr-xr-x@ 20 fabbri  staff     680 Jan 26  2010 HarvardOxford</div>

<div>-rw-r--r--   1 fabbri  staff    4335 Aug  7  2007 HarvardOxford-Cortical.xml</div><div>-rw-r--r--@  1 fabbri  staff    1968 Aug  7  2007 HarvardOxford-Subcortical.xml</div><div>drwxr-xr-x@ 19 fabbri  staff     646 Jan 26  2010 JHU</div>

<div>-rw-r--r--@  1 fabbri  staff    4622 Aug 15  2007 JHU-labels.xml</div><div>-rw-r--r--@  1 fabbri  staff    2094 Aug  6  2007 JHU-tracts.xml</div><div>drwxr-xr-x@ 10 fabbri  staff     340 Jan 26  2010 Juelich</div><div>

-rw-r--r--   1 fabbri  staff   10346 Nov  3  2009 Juelich.xml</div><div>drwxr-xr-x@ 11 fabbri  staff     374 Jan 26  2010 MNI</div><div>-rw-r--r--   1 fabbri  staff     987 Aug  7  2007 MNI.xml</div><div>drwxr-xr-x@  4 fabbri  staff     136 Jan 26  2010 Talairach</div>

<div>-rw-r--r--@  1 fabbri  staff  121710 Aug  7  2007 Talairach.xml</div><div>drwxr-xr-x@ 10 fabbri  staff     340 Jan 26  2010 Thalamus</div><div>-rw-r--r--@  1 fabbri  staff     985 Aug  7  2007 Thalamus.xml</div><div>

drwxr-xr-x   5 fabbri  staff     170 Oct 18 12:33 aai</div><div>-rw-r--r--@  1 fabbri  staff    5808 Oct 18 13:12 aal.xml</div><div>drwxr-xr-x@  7 fabbri  staff     238 Jan 26  2010 bin</div><div><br></div><div>./Cerebellum:</div>

<div>total 3608</div><div>-rw-r--r--@ 1 fabbri  staff   44555 Feb 27  2009 Cerebellum-MNIflirt-maxprob-thr0-1mm.nii.gz</div><div>-rw-r--r--@ 1 fabbri  staff    9433 Feb 27  2009 Cerebellum-MNIflirt-maxprob-thr0-2mm.nii.gz</div>

<div>-rw-r--r--@ 1 fabbri  staff   34698 Feb 27  2009 Cerebellum-MNIflirt-maxprob-thr25-1mm.nii.gz</div><div>-rwxr-xr-x@ 1 fabbri  staff    6926 Feb 25  2009 Cerebellum-MNIflirt-maxprob-thr25-2mm.nii.gz</div><div>-rw-r--r--@ 1 fabbri  staff   30946 Feb 27  2009 Cerebellum-MNIflirt-maxprob-thr50-1mm.nii.gz</div>

<div>-rw-r--r--@ 1 fabbri  staff    6245 Feb 27  2009 Cerebellum-MNIflirt-maxprob-thr50-2mm.nii.gz</div><div>-rw-r--r--@ 1 fabbri  staff  712945 Feb 26  2009 Cerebellum-MNIflirt-prob-1mm.nii.gz</div><div>-rwxr-xr-x@ 1 fabbri  staff   96399 Feb 24  2009 Cerebellum-MNIflirt-prob-2mm.nii.gz</div>

<div>-rw-r--r--@ 1 fabbri  staff   41376 Feb 27  2009 Cerebellum-MNIfnirt-maxprob-thr0-1mm.nii.gz</div><div>-rw-r--r--@ 1 fabbri  staff    8343 Feb 27  2009 Cerebellum-MNIfnirt-maxprob-thr0-2mm.nii.gz</div><div>-rw-r--r--@ 1 fabbri  staff   34221 Feb 27  2009 Cerebellum-MNIfnirt-maxprob-thr25-1mm.nii.gz</div>

<div>-rw-r--r--@ 1 fabbri  staff    6681 Feb 25  2009 Cerebellum-MNIfnirt-maxprob-thr25-2mm.nii.gz</div><div>-rw-r--r--@ 1 fabbri  staff   32621 Feb 27  2009 Cerebellum-MNIfnirt-maxprob-thr50-1mm.nii.gz</div><div>-rw-r--r--@ 1 fabbri  staff    6420 Feb 27  2009 Cerebellum-MNIfnirt-maxprob-thr50-2mm.nii.gz</div>

<div>-rw-r--r--@ 1 fabbri  staff  651100 Feb 26  2009 Cerebellum-MNIfnirt-prob-1mm.nii.gz</div><div>-rw-r--r--@ 1 fabbri  staff   93252 Feb 24  2009 Cerebellum-MNIfnirt-prob-2mm.nii.gz</div><div><br></div><div>./HarvardOxford:</div>

<div>total 16760</div><div>-rw-r--r--@ 1 fabbri  staff   180388 Aug  7  2007 HarvardOxford-cort-maxprob-thr0-1mm.nii.gz</div><div>-rw-r--r--@ 1 fabbri  staff    36850 Aug  7  2007 HarvardOxford-cort-maxprob-thr0-2mm.nii.gz</div>

<div>-rw-r--r--@ 1 fabbri  staff   146506 Aug  7  2007 HarvardOxford-cort-maxprob-thr25-1mm.nii.gz</div><div>-rw-r--r--@ 1 fabbri  staff    29113 Aug  7  2007 HarvardOxford-cort-maxprob-thr25-2mm.nii.gz</div><div>-rw-r--r--@ 1 fabbri  staff   129144 Aug  7  2007 HarvardOxford-cort-maxprob-thr50-1mm.nii.gz</div>

<div>-rw-r--r--@ 1 fabbri  staff    22629 Aug  7  2007 HarvardOxford-cort-maxprob-thr50-2mm.nii.gz</div><div>-rw-r--r--@ 1 fabbri  staff  3412276 Aug  7  2007 HarvardOxford-cort-prob-1mm.nii.gz</div><div>-rw-r--r--@ 1 fabbri  staff   513170 Aug  7  2007 HarvardOxford-cort-prob-2mm.nii.gz</div>

<div>-rw-r--r--@ 1 fabbri  staff   143394 Aug  7  2007 HarvardOxford-sub-maxprob-thr0-1mm.nii.gz</div><div>-rw-r--r--@ 1 fabbri  staff    28758 Aug  7  2007 HarvardOxford-sub-maxprob-thr0-2mm.nii.gz</div><div>-rw-r--r--@ 1 fabbri  staff   137877 Aug  7  2007 HarvardOxford-sub-maxprob-thr25-1mm.nii.gz</div>

<div>-rw-r--r--@ 1 fabbri  staff    26686 Aug  7  2007 HarvardOxford-sub-maxprob-thr25-2mm.nii.gz</div><div>-rw-r--r--@ 1 fabbri  staff   164702 Aug  7  2007 HarvardOxford-sub-maxprob-thr50-1mm.nii.gz</div><div>-rw-r--r--@ 1 fabbri  staff    31694 Aug  7  2007 HarvardOxford-sub-maxprob-thr50-2mm.nii.gz</div>

<div>-rw-r--r--@ 1 fabbri  staff  3097063 Aug  7  2007 HarvardOxford-sub-prob-1mm.nii.gz</div><div>-rw-r--r--@ 1 fabbri  staff   430411 Aug  7  2007 HarvardOxford-sub-prob-2mm.nii.gz</div><div>-rw-r--r--  1 fabbri  staff       60 May 22  2007 labels</div>

<div>-rwxr-xr-x@ 1 fabbri  staff      209 May 22  2007 relabel</div><div><br></div><div>./JHU:</div><div>total 27168</div><div>-rw-r--r--@ 1 fabbri  staff  1127989 Aug 12  2007 JHU-ICBM-DWI-1mm.nii.gz</div><div>-rw-r--r--@ 1 fabbri  staff   206277 Aug 12  2007 JHU-ICBM-DWI-2mm.nii.gz</div>

<div>-rw-r--r--@ 1 fabbri  staff  6748509 Aug  6  2007 JHU-ICBM-FA-1mm.nii.gz</div><div>-rw-r--r--@ 1 fabbri  staff   922943 Aug  6  2007 JHU-ICBM-FA-2mm.nii.gz</div><div>-rw-r--r--@ 1 fabbri  staff  2685506 Aug 12  2007 JHU-ICBM-T2-1mm.nii.gz</div>

<div>-rw-r--r--@ 1 fabbri  staff   434038 Aug 12  2007 JHU-ICBM-T2-2mm.nii.gz</div><div>-rw-r--r--@ 1 fabbri  staff        0 Aug  6  2007 JHU-ICBM-WhiteMatter-labels-2mm.nii.gz</div><div>-rw-r--r--@ 1 fabbri  staff   286344 Aug  6  2007 JHU-ICBM-tracts-maxprob-thr0-1mm.nii.gz</div>

<div>-rw-r--r--@ 1 fabbri  staff    34985 Aug  6  2007 JHU-ICBM-tracts-maxprob-thr0-2mm.nii.gz</div><div>-rw-r--r--@ 1 fabbri  staff    53988 Aug  6  2007 JHU-ICBM-tracts-maxprob-thr25-1mm.nii.gz</div><div>-rw-r--r--@ 1 fabbri  staff     7161 Aug  6  2007 JHU-ICBM-tracts-maxprob-thr25-2mm.nii.gz</div>

<div>-rw-r--r--@ 1 fabbri  staff    26051 Aug  6  2007 JHU-ICBM-tracts-maxprob-thr50-1mm.nii.gz</div><div>-rw-r--r--@ 1 fabbri  staff     2787 Aug  6  2007 JHU-ICBM-tracts-maxprob-thr50-2mm.nii.gz</div><div>-rw-r--r--@ 1 fabbri  staff  1097811 Aug  6  2007 JHU-ICBM-tracts-prob-1mm.nii.gz</div>

<div>-rw-r--r--@ 1 fabbri  staff   181917 Aug  6  2007 JHU-ICBM-tracts-prob-2mm.nii.gz</div><div>-rw-r--r--@ 1 fabbri  staff    52093 Aug  7  2007 JHU-WhiteMatter-labels-1mm.nii.gz</div><div>-rw-r--r--@ 1 fabbri  staff     9611 Aug  7  2007 JHU-WhiteMatter-labels-2mm.nii.gz</div>

<div><br></div><div>./Juelich:</div><div>total 9296</div><div>-rw-r--r--@ 1 fabbri  staff   208007 Oct 27  2009 Juelich-maxprob-thr0-1mm.nii.gz</div><div>-rw-r--r--@ 1 fabbri  staff    38194 Oct 27  2009 Juelich-maxprob-thr0-2mm.nii.gz</div>

<div>-rw-r--r--@ 1 fabbri  staff   162725 Oct 27  2009 Juelich-maxprob-thr25-1mm.nii.gz</div><div>-rw-r--r--@ 1 fabbri  staff    28787 Oct 27  2009 Juelich-maxprob-thr25-2mm.nii.gz</div><div>-rw-r--r--@ 1 fabbri  staff   126683 Oct 27  2009 Juelich-maxprob-thr50-1mm.nii.gz</div>

<div>-rw-r--r--@ 1 fabbri  staff    20766 Oct 27  2009 Juelich-maxprob-thr50-2mm.nii.gz</div><div>-rw-r--r--@ 1 fabbri  staff  3573573 Oct 27  2009 Juelich-prob-1mm.nii.gz</div><div>-rw-r--r--@ 1 fabbri  staff   581690 Nov  3  2009 Juelich-prob-2mm.nii.gz</div>

<div><br></div><div>./MNI:</div><div>total 5384</div><div>-rw-r--r--  1 fabbri  staff      473 Aug  7  2007 DO</div><div>-rw-r--r--@ 1 fabbri  staff   127787 Aug  7  2007 MNI-maxprob-thr0-1mm.nii.gz</div><div>-rw-r--r--@ 1 fabbri  staff    26638 Aug  7  2007 MNI-maxprob-thr0-2mm.nii.gz</div>

<div>-rw-r--r--@ 1 fabbri  staff   139095 Aug  7  2007 MNI-maxprob-thr25-1mm.nii.gz</div><div>-rw-r--r--@ 1 fabbri  staff    29427 Jun  6  2007 MNI-maxprob-thr25-2mm.nii.gz</div><div>-rw-r--r--@ 1 fabbri  staff   147027 Aug  7  2007 MNI-maxprob-thr50-1mm.nii.gz</div>

<div>-rw-r--r--@ 1 fabbri  staff    31077 Jun  6  2007 MNI-maxprob-thr50-2mm.nii.gz</div><div>-rw-r--r--@ 1 fabbri  staff  1948363 Aug  7  2007 MNI-prob-1mm.nii.gz</div><div>-rw-r--r--@ 1 fabbri  staff   289044 Jun  6  2007 MNI-prob-2mm.nii.gz</div>

<div><br></div><div>./Talairach:</div><div>total 968</div><div>-rw-r--r--@ 1 fabbri  staff  430529 Aug  8  2007 Talairach-labels-1mm.nii.gz</div><div>-rw-r--r--@ 1 fabbri  staff   60463 Aug  3  2007 Talairach-labels-2mm.nii.gz</div>

<div><br></div><div>./Thalamus:</div><div>total 600</div><div>-rw-r--r--@ 1 fabbri  staff   19605 Aug  7  2007 Thalamus-maxprob-thr0-1mm.nii.gz</div><div>-rw-r--r--@ 1 fabbri  staff    3384 Aug  7  2007 Thalamus-maxprob-thr0-2mm.nii.gz</div>

<div>-rw-r--r--@ 1 fabbri  staff   14945 Aug  7  2007 Thalamus-maxprob-thr25-1mm.nii.gz</div><div>-rw-r--r--@ 1 fabbri  staff    2396 Aug  7  2007 Thalamus-maxprob-thr25-2mm.nii.gz</div><div>-rw-r--r--@ 1 fabbri  staff   13296 Aug  7  2007 Thalamus-maxprob-thr50-1mm.nii.gz</div>

<div>-rw-r--r--@ 1 fabbri  staff    2024 Aug  7  2007 Thalamus-maxprob-thr50-2mm.nii.gz</div><div>-rw-r--r--@ 1 fabbri  staff  207512 Aug  7  2007 Thalamus-prob-1mm.nii.gz</div><div>-rw-r--r--@ 1 fabbri  staff   31649 Aug  7  2007 Thalamus-prob-2mm.nii.gz</div>

<div><br></div><div>./aai:</div><div>total 7064</div><div>-rw-r--r--@ 1 fabbri  staff     2713 Oct 17 12:11 aal.nii.txt</div><div>-rw-r--r--  1 fabbri  staff  3610868 Oct 18 11:57 aal_2mm.nii</div><div><br></div><div>./bin:</div>

<div>total 40</div><div>-rwxr-xr-x@ 1 fabbri  staff  235 Aug  5  2007 addlut</div><div>-rw-r--r--@ 1 fabbri  staff   33 Jul 10  2007 eye.mat</div><div>-rwxr-xr-x@ 1 fabbri  staff  654 Aug  5  2007 locate-centres</div><div>

-rwxr-xr-x@ 1 fabbri  staff  627 Aug  6  2007 locate-label-centres</div><div>-rwxr-xr-x@ 1 fabbri  staff  650 Mar 17  2008 threshold</div><div><br></div><div><br></div><div><br></div><div><span style="color:rgb(183, 38, 18)">Thank you for your help.</span></div>

<div><span style="color:rgb(183, 38, 18)"><br></span></div><div><span style="color:rgb(183, 38, 18)">Serena.</span></div></div><div><span style="color:rgb(183, 38, 18)"><br></span></div></blockquote></div><div><div>
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</div><div><br></div><div><br></div><div><br><div class="gmail_quote">On Mon, Oct 18, 2010 at 4:09 PM, David Flitney <span dir="ltr">&lt;<a href="mailto:[log in to unmask]" target="_blank"><a href="/cgi-bin/wa-jisc.exe?LOGON=A3%3Dind1010%26L%3DFSL%26E%3Dquoted-printable%26P%3D2059377%26B%3D--001485f629caf075a90492f94791%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>Hi</div><div><div><br></div><div>On 18 Oct 2010, at 12:25, sere f wrote:</div>
</div><div><div><div><br><blockquote type="cite"><div>Dear FSL users,</div><div><br></div><div>I am trying to add an atlas (and xml file ) in $FSL/data/atlases. </div><div>I have followed the instructions in  <a href="http://www.fmrib.ox.ac.uk/fsl/data/atlas-reference.html" target="_blank">http://www.fmrib.ox.ac.uk/fsl/data/atlas-reference.html</a>  to create xlm file, but FSL viewer does not find labels. </div>


</blockquote><div><br></div></div>Could you send me the output of:<div><br></div><div>ls -lR $FSL/data/atlases</div><div><br></div><div>along with a listing of your XML file.</div><div><div><br></div><blockquote type="cite">



<div>In fact  in &quot;the atlas selection dialog&quot; window this file does not appear.</div><div>Where do I wrong? Could you give me some help please? </div></blockquote><div><br></div></div><div>If the XML file is in the atlases directory then the name &quot;Blah&quot; - from &lt;name&gt;Blah&lt;/name&gt; - should appear in the selection dialog.</div>


<div><br></div><div><div></div></div><blockquote type="cite"><div><br></div><div>Thank you.</div><div><br></div><div>Serena.</div>
</blockquote></div><br><div>
<span style="border-collapse:separate;color:rgb(0, 0, 0);font-family:Helvetica;font-size:12px;font-style:normal;font-variant:normal;font-weight:normal;letter-spacing:normal;line-height:normal;text-align:auto;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px"><div>


<div style="margin-top:0px;margin-right:0px;margin-bottom:0px;margin-left:0px">-- </div><div style="margin-top:0px;margin-right:0px;margin-bottom:0px;margin-left:0px">Dave Flitney, IT Manager</div><div style="margin-top:0px;margin-right:0px;margin-bottom:0px;margin-left:0px">


Oxford Centre for Functional MRI of the Brain</div><div style="margin-top:0px;margin-right:0px;margin-bottom:0px;margin-left:0px">E:<a href="mailto:[log in to unmask]" target="_blank"><a href="/cgi-bin/wa-jisc.exe?LOGON=A3%3Dind1010%26L%3DFSL%26E%3Dquoted-printable%26P%3D2059377%26B%3D--001485f629caf075a90492f94791%26T%3Dtext%252Fhtml%3B%2520charset%3DISO-8859-1%26pending%3D" target="_parent" >[log in to unmask]</a></a> W:+44-1865-222713 F:+44-1865-222717</div>


<div style="margin-top:0px;margin-right:0px;margin-bottom:0px;margin-left:0px">URL: <a href="http://www.fmrib.ox.ac.uk/~flitney" target="_blank">http://www.fmrib.ox.ac.uk/~flitney</a></div><div><br></div></div></span><br>



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</div></div><span>&lt;aal.xml&gt;</span></blockquote></div><div class="im"><br><div>
<span style="border-collapse:separate;color:rgb(0, 0, 0);font-family:Helvetica;font-size:12px;font-style:normal;font-variant:normal;font-weight:normal;letter-spacing:normal;line-height:normal;text-align:auto;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px"><div>
<div style="margin-top:0px;margin-right:0px;margin-bottom:0px;margin-left:0px">-- </div><div style="margin-top:0px;margin-right:0px;margin-bottom:0px;margin-left:0px">Dave Flitney, IT Manager</div><div style="margin-top:0px;margin-right:0px;margin-bottom:0px;margin-left:0px">
Oxford Centre for Functional MRI of the Brain</div><div style="margin-top:0px;margin-right:0px;margin-bottom:0px;margin-left:0px">E:<a href="mailto:[log in to unmask]" target="_blank"><a href="/cgi-bin/wa-jisc.exe?LOGON=A3%3Dind1010%26L%3DFSL%26E%3Dquoted-printable%26P%3D2059377%26B%3D--001485f629caf075a90492f94791%26T%3Dtext%252Fhtml%3B%2520charset%3DISO-8859-1%26pending%3D" target="_parent" >[log in to unmask]</a></a> W:+44-1865-222713 F:+44-1865-222717</div>
<div style="margin-top:0px;margin-right:0px;margin-bottom:0px;margin-left:0px">URL: <a href="http://www.fmrib.ox.ac.uk/~flitney" target="_blank">http://www.fmrib.ox.ac.uk/~flitney</a></div><div><br></div></div></span><br>

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