<div dir="ltr">Hi <span style="font-family:arial,sans-serif;font-size:12.727272033691406px">Rômulo,</span><div><font face="arial, sans-serif"><br></font></div><div><font face="arial, sans-serif">Thanks for your reply. Actually, Vivien had already converted those images from matlab format to mhd. I double checked them and he did indeed account for the signed/unsigned HU related issues. Let me know and I could put one of the images up on dropbox. I'm looking at their breath-hold copd data - not 4dct.</font></div>
<div><font face="arial, sans-serif"><br></font></div><div><font face="arial, sans-serif">Best wishes,</font></div><div><font face="arial, sans-serif"><br></font></div><div><font face="arial, sans-serif">Bilal<br></font><table cellpadding="0" class="" style="font-family:arial,sans-serif;font-size:12.727272033691406px">
<tbody><tr class=""><td class="" style="width:449.2755432128906px"><br></td></tr></tbody></table></div></div><div class="gmail_extra"><br><br><div class="gmail_quote">On 23 October 2013 21:41, Rômulo Pinho <span dir="ltr"><<a href="mailto:romulopinho@yahoo.com.br" target="_blank">romulopinho@yahoo.com.br</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div bgcolor="#FFFFFF" text="#000000">
Hello, Bilal,<br>
<br>
I'd have to verify this (maybe Vivien can also comment on that), but
I think the dir-lab data are not in HU, i.e., the grey values are
all positive, from 0 to 4096. The algorithms in clitkExtractLung
apply some thresholding operations that depend on a data set in HU,
roughly from -1024 to 3072. <br>
<br>
To cope with it, you can either play with the parameters
seedPreProcessingThreshold and upperThresholdForTrachea in
clitkExtratLung (depending on TYPE)<br>
"upperThresholdForTrachea" - "0: Initial upper threshold for
trachea" default="-900"<br>
"seedPreProcessingThreshold" - "1: Threshold for the
pre-processing step of the algorithm" default="-400"<br>
<br>
or, to be on the safe side, shift your grey values prior to
launching clitkExtractLung. You can do it by creating an image with
-1024 everywhere (clitkCreateImage does the job) and then applying
the shift by adding the two images with clitkImageArithm. <br>
<br>
In any case, using --verboseRG might also give some extra insights.<br>
<br>
I hope this helps!<br>
<br>
Best,<br>
Rômulo<div><div class="h5"><br>
<br>
<div>On 23/10/2013 14:15, Bilal Tahir wrote:<br>
</div>
<blockquote type="cite">
<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><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/displayApproved?result=20110708160218_86_CREATIS_CLB_Lyon_graphcut&file=20110708160218_86_CREATIS_CLB_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><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.fr/rio</a></font></span>
<div>
<div><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>
</div>
</div>
</div>
<br>
<fieldset></fieldset>
<br>
<pre>_______________________________________________
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</pre>
</blockquote>
<br>
</div></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>
</div>
</div>