<div dir="ltr">Thanks Vivien,<div><br></div><div>I've got passed the .afdb stage. However I'm getting errors at the 'search for trachea' stage for both the original and LOLA11 algorithms. The dataset is the inspiration scans for patient 1 of the dir-lab copd data. </div>
<div><br></div><div><span style="background-color:rgb(255,0,0)">1) LOLA 11:</span></div><div><span style="background-color:rgb(255,0,0)"><br></span></div><div><div><span style="background-color:rgb(255,0,0)">[md1bat@testnode02 mhd]$ clitkExtractLung --verboseStep 1 -i copd1_00.mhd -a default.afdb -o 00_lungs.mhd --type=1</span></div>
<div><span style="background-color:rgb(255,0,0)">Step 1 -- Copy and crop input image to 'patient' extends</span></div><div><span style="background-color:rgb(255,0,0)">Step 2 -- Set background to initial image</span></div>
<div><span style="background-color:rgb(255,0,0)">Step 3 -- Remove Air</span></div><div><span style="background-color:rgb(255,0,0)">Step 4 -- Search for the trachea</span></div><div><span style="background-color:rgb(255,0,0)"><br>
</span></div><div><span style="background-color:rgb(255,0,0)">itk::InvalidRequestedRegionError (0x2bca660)</span></div><div><span style="background-color:rgb(255,0,0)">Location: "unknown" </span></div><div><span style="background-color:rgb(255,0,0)">File: /home/md1bat/Source/itk/Modules/Core/Common/src/itkDataObject.cxx</span></div>
<div><span style="background-color:rgb(255,0,0)">Line: 411</span></div><div><span style="background-color:rgb(255,0,0)">Description: Requested region is (at least partially) outside the largest possible region.</span></div>
</div><div><span style="background-color:rgb(255,0,0)"><br></span></div><div><span style="background-color:rgb(255,0,0)">2) Original (type=0)</span></div><div><span style="background-color:rgb(255,0,0)"><br></span></div><div>
<div><span style="background-color:rgb(255,0,0)">[md1bat@testnode02 mhd]$ clitkExtractLung --verboseStep 1 -i copd1_00.mhd -a default.afdb -o 00_lungs.mhd --type=0</span></div><div><span style="background-color:rgb(255,0,0)">Step 1 -- Copy and crop input image to 'patient' extends</span></div>
<div><span style="background-color:rgb(255,0,0)">Step 2 -- Set background to initial image</span></div><div><span style="background-color:rgb(255,0,0)">Step 3 -- Remove Air</span></div><div><span style="background-color:rgb(255,0,0)">Step 4 -- Search for the trachea</span></div>
<div><span style="background-color:rgb(255,0,0)"> The volume of the trachea (4035.53 cc) seems not correct. I skip some slices (0) and restart to find seeds.</span></div><div><span style="background-color:rgb(255,0,0)"> The volume of the trachea (4037.01 cc) seems not correct. I skip some slices (5) and restart to find seeds.</span></div>
<div><span style="background-color:rgb(255,0,0)"> The volume of the trachea (4036.86 cc) seems not correct. I skip some slices (10) and restart to find seeds.</span></div><div><span style="background-color:rgb(255,0,0)"> The volume of the trachea (4036.39 cc) seems not correct. I skip some slices (15) and restart to find seeds.</span></div>
<div><span style="background-color:rgb(255,0,0)"> The volume of the trachea (4036.07 cc) seems not correct. I skip some slices (20) and restart to find seeds.</span></div><div><span style="background-color:rgb(255,0,0)"> The volume of the trachea (4035.31 cc) seems not correct. I skip some slices (25) and restart to find seeds.</span></div>
<div><span style="background-color:rgb(255,0,0)"> The volume of the trachea (4035.54 cc) seems not correct. I skip some slices (30) and restart to find seeds.</span></div><div><span style="background-color:rgb(255,0,0)"> The volume of the trachea (4035.49 cc) seems not correct. I skip some slices (35) and restart to find seeds.</span></div>
<div><span style="background-color:rgb(255,0,0)"> The volume of the trachea (4035.39 cc) seems not correct. I skip some slices (40) and restart to find seeds.</span></div><div><span style="background-color:rgb(255,0,0)"> The volume of the trachea (4035.57 cc) seems not correct. I skip some slices (45) and restart to find seeds.</span></div>
<div><span style="background-color:rgb(255,0,0)"> The volume of the trachea (4035.69 cc) seems not correct. I skip some slices (50) and restart to find seeds.</span></div><div><span style="background-color:rgb(255,0,0)"> The volume of the trachea (4036.09 cc) seems not correct. I skip some slices (55) and restart to find seeds.</span></div>
<div><span style="background-color:rgb(255,0,0)"> The volume of the trachea (4036.34 cc) seems not correct. I skip some slices (60) and restart to find seeds.</span></div><div><span style="background-color:rgb(255,0,0)">2 : Number of slices to skip to find trachea too high = 65</span></div>
<div><span style="background-color:rgb(255,0,0)"><br></span></div><div><span style="background-color:rgb(255,0,0)">itk::ExceptionObject (0x377f970)</span></div><div><span style="background-color:rgb(255,0,0)">Location: "Unknown" </span></div>
<div><span style="background-color:rgb(255,0,0)">File: /home/md1bat/Source/vv/segmentation/clitkExtractLungFilter.txx</span></div><div><span style="background-color:rgb(255,0,0)">Line: 266</span></div><div><span style="background-color:rgb(255,0,0)">Description: No seeds for trachea... Aborting.</span></div>
</div><div><span style="background-color:rgb(255,0,0)"><br></span></div><div><span style="background-color:rgb(255,0,0)">3) Manually setting a higher number of slices than 65</span></div><div><span style="background-color:rgb(255,0,0)"><br>
</span></div><div><div><span style="background-color:rgb(255,0,0)">[md1bat@testnode02 mhd]$ clitkExtractLung --verbose 1 -i copd1_00.mhd -a default.afdb -o 00_lungs.mhd --skipslices=90</span></div><div><span style="background-color:rgb(255,0,0)">Input is 3D short.</span></div>
<div><span style="background-color:rgb(255,0,0)">Reading [copd1_00.mhd] ... </span></div><div><span style="background-color:rgb(255,0,0)">2 : Number of slices to skip to find trachea too high = 95</span></div><div><span style="background-color:rgb(255,0,0)"><br>
</span></div><div><span style="background-color:rgb(255,0,0)">itk::ExceptionObject (0x3a379d0)</span></div><div><span style="background-color:rgb(255,0,0)">Location: "Unknown" </span></div><div><span style="background-color:rgb(255,0,0)">File: /home/md1bat/Source/vv/segmentation/clitkExtractLungFilter.txx</span></div>
<div><span style="background-color:rgb(255,0,0)">Line: 266</span></div><div><span style="background-color:rgb(255,0,0)">Description: No seeds for trachea... Aborting.</span></div></div><div><br></div><div>As you can see, I keep failing at the search trachea stage even by trying various different options for slices to skip for the trachea. Please let me know if you have any suggestions that can help.</div>
<div><br></div><div>Best wishes,</div><div><br></div><div>Bilal</div><div class="gmail_extra"><br><br><div class="gmail_quote">On 23 October 2013 16:51, Vivien Delmon <span dir="ltr"><<a href="mailto:vivien.delmon@creatis.insa-lyon.fr" target="_blank">vivien.delmon@creatis.insa-lyon.fr</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">On 10/18/2013 12:08 AM, Bilal Tahir wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Dear VV community,<br>
<br>
...<div class="im"><br>
<br>
Also I would like to know if the LOLA11 paper below is the correct<br>
reference if I decide to use your method for publications?<br>
<br>
<a href="http://lola11.com/Results/displayApproved?result=20110708160218_86_CREATIS_CLB_Lyon_graphcut&file=20110708160218_86_CREATIS_CLB_Lyon_graphcut_lola11.pdf" target="_blank">http://lola11.com/Results/<u></u>displayApproved?result=<u></u>20110708160218_86_CREATIS_CLB_<u></u>Lyon_graphcut&file=<u></u>20110708160218_86_CREATIS_CLB_<u></u>Lyon_graphcut_lola11.pdf</a><br>
</div></blockquote>
<br>
Part of the work presented in this paper have been implemented in clitkExtractLung but you need to explicitly ask the tool to use it :<br>
<br>
Step 2 : find trachea:<br>
--type=INT trachea finding algorithm (0: original; 1:LOLA11) (default=`0')<br>
<br>
The second part about graphcut labeling were not included in this tool since we never really need to separate lungs.<br>
<br>
Last time I tried to activate --type=1 it failed, I will have a look at it one day.<br>
<br>
As far as I know there is no other paper that describe what we have implemented in this tool, so this paper should be the one to cite.<span class="HOEnZb"><font color="#888888"><br>
<br>
-- <br>
Vivien Delmon<br>
PhD student at CREATIS, Lyon<br>
Supported by ANRT and ELEKTA<br>
<a href="http://www.creatis.insa-lyon.fr/rio" target="_blank">http://www.creatis.insa-lyon.<u></u>fr/rio</a></font></span><div class="HOEnZb"><div class="h5"><br>
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</div></div></blockquote></div><br><br clear="all"><div><br></div>-- <br><div dir="ltr">Bilal Tahir,<div>James Morrison Researcher in Radiotherapy Imaging,</div><div>Department of Clinical Oncology,</div><div>University of Sheffield</div>
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