Hi Bruce,<div><br></div><div>Yes. I am using voxel coordinates. </div><div><br></div><div>The command line is:</div><div>mri_fill /space/data/shayo/cooked/test2/mri/wm.nii /space/data/shayo/cooked/test2/mri/filled.nii -CV 122 116 91</div>

<div>(I also gave the pons values, but it didn&#39;t seem to change anything).</div><div><br></div><div>-- Shay</div><div>Tsao lab</div><div>Caltech</div><div><br><br><div class="gmail_quote">On Thu, Jun 7, 2012 at 6:55 PM, Bruce Fischl <span dir="ltr">&lt;<a href="mailto:fischl@nmr.mgh.harvard.edu" target="_blank">fischl@nmr.mgh.harvard.edu</a>&gt;</span> wrote:<br>

<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div bgcolor="#FFFFFF"><div>What&#39;s your command line? Are you using voxel coords?<br><br><br></div><div><div class="h5">

<div><br>On Jun 7, 2012, at 9:52 PM, Shay Ohayon &lt;<a href="mailto:shay.ohayon@gmail.com" target="_blank">shay.ohayon@gmail.com</a>&gt; wrote:<br><br></div><div></div><blockquote type="cite"><div>Hi,<div><br></div><div>

I am having problem getting mri_fill to run on one of my volumes (it did work with another monkey, so I assume I am running things right).</div><div>I am using v5.0 (but it also happens on 5.1).</div>

<div>The input is a monkey wm file with specified coordinates for the corpus callosum.</div><div>The error I get is: &quot;could not find corpus callosum&quot; (see full log below).</div><div>The input volume is available for download <a href="http://tsaolab.caltech.edu/sites/default/files/wm.mgz" target="_blank">here </a>(<a href="http://tsaolab.caltech.edu/sites/default/files/wm.mgz" target="_blank">http://tsaolab.caltech.edu/sites/default/files/wm.mgz</a>)</div>



<div><br></div><div>Any takers?  I tried various different coordinates and all of them fail.</div><div>A hint may be this statement: &quot;find_cutting_plane:seed point not in structure! Searching neighborhood...&quot;</div>



<div>which I don&#39;t fully understand as the point given is inside a connected component...</div><div><br></div><div>Many thanks,</div><div><br></div><div>Shay </div><div>Tsao Lab</div><div>Caltech</div><div><br></div>


<div>
<br></div><div><br></div><div><br></div><div>---------------------------</div><div><div><br></div><div>reading input volume...done.</div><div>searching for cutting planes...INFO: volume does not have linear_transform set nor lta is given by option.-xform.</div>



<div>INFO: use identity matrix as the talairach transform.</div><div>INFO: use src volume parameters for the talairach volume.</div><div>voxel to talairach voxel transform</div><div> 1.000   0.000   0.000   0.000;</div><div>



 0.000   1.000   0.000   0.000;</div><div> 0.000   0.000   1.000   0.000;</div><div> 0.000   0.000   0.000   1.000;</div><div>find_cutting_plane:seed point not in structure! Searching neighborhood...</div><div>Looking for area (min, max) = (350, 1400)</div>



<div>area[0] = 1 (min = 350, max = 1400), aspect = 1.00 (min = 0.10, max = 0.75)</div><div>need search nearby</div><div>using +/- offset search region where offset is 3.....</div><div>using +/- offset search region where offset is 6.....</div>



<div>using +/- offset search region where offset is 9.....</div><div>using +/- offset search region where offset is 12.....</div><div>using +/- offset search region where offset is 15.....</div><div>using +/- offset search region where offset is 18.....</div>



<div>using +/- offset search region where offset is 21.....</div><div>using +/- offset search region where offset is 24.....</div><div>using +/- offset search region where offset is 27.....</div><div>using +/- offset search region where offset is 30.....</div>



<div>using +/- offset search region where offset is 33.....</div><div>using +/- offset search region where offset is 36.....</div><div>using +/- offset search region where offset is 39.....</div><div>using +/- offset search region where offset is 42.....</div>



<div>using +/- offset search region where offset is 45.....</div><div>using +/- offset search region where offset is 48.....</div><div>/space/opt/freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0/bin/mri_fill: could not find corpus callosum</div>



<div>/space/opt/freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0/bin/mri_fill /space/data/shayo/cooked/test2/mri/wm.nii /space/data/shayo/cooked/test2/mri/filled.nii -CV 128 117 91: Signal 124</div></div><div><br></div>


<div>
<br></div><div><br></div>
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