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Ok, Bilal, thanks for the update.<br>
It's hard for me to check it now, because I'd have to
download/compile the entire VV project plus ITK, VTK, etc.<br>
In any case, I still suggest you to play with the parameters of
clitkExtracLung related to the extraction of the trachea. You can
also post the output of --verboseRG on the list.<br>
Best,<br>
Rômulo<br>
<br>
<div class="moz-cite-prefix">On 23/10/2013 19:20, Bilal Tahir wrote:<br>
</div>
<blockquote
cite="mid:CAFZ9P6G_dEiTWKqQvJiZ_8T=2ue--Hi_VK6-TxWHLy=qOCWkhQ@mail.gmail.com"
type="cite">
<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>
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<div class="gmail_extra"><br>
<br>
<div class="gmail_quote">On 23 October 2013 21:41, Rômulo Pinho
<span dir="ltr"><<a moz-do-not-send="true"
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
moz-do-not-send="true"
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 moz-do-not-send="true"
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 moz-do-not-send="true"
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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href="mailto:vv@creatis.insa-lyon.fr"
target="_blank">vv@creatis.insa-lyon.fr</a><br>
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href="http://www.creatis.insa-lyon.fr/mailman/listinfo/vv"
target="_blank">http://www.creatis.insa-lyon.fr/mailman/listinfo/vv</a><br>
</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>
</blockquote>
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