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Hello, Bilal,<br>
I'm posting your results back to the list. You could also post the
output of type LOLA11.<br>
But I'd say there's indeed a thresholding problem somewhere... I'd
suggest you to inspect your image (e.g., with VV) to have an idea
about the grey values inside the trachea and then adjust the
parameters of clitkExtractImage accordingly. Another possibility is
that your image is very noisy and, as such, if you have a short
range of grey values for the threshold, you segment too little,
possibly resulting in disconnected regions. If by contrast you have
a large range of values, you segment too much, and this will ruin
both types of trachea detection algorithm... If the image is indeed
noisy, you can try to apply a smoothing filter to it. <br>
I regret I can't open the image to check it myself.<br>
Hope this helps.<br>
Cheers,<br>
Rômulo<br>
<br>
<div class="moz-cite-prefix">On 23/10/2013 22:19, Bilal Tahir wrote:<br>
</div>
<blockquote
cite="mid:CAFZ9P6GeGMyDeqGdfoQ2gAfYrYhdVFRpq-qy_b8TkENwk7yguA@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">Below is my --verboseRG
output. I am still looking into it to see where it is
breaking down for the trachea. Let me know if you notice any
obvious reasons:</font>
<div>
<div><br>
</div>
<div>[md1bat@testnode01 mhd]$ clitkExtractLung --verboseRG 1
-i copd1_00.mhd -a default.afdb -o 00_lungs.mhd</div>
<div>Initial region size using thresholds [-2000, -900], is
4132644...</div>
<div>Increasing upper threshold to -836, size is
5983512(previously 4132644) ...</div>
<div>Increasing upper threshold to -772, size is
6367804(previously 5983512) ...</div>
<div>Increasing upper threshold to -708, size is
6543232(previously 6367804) ...</div>
<div>Increasing upper threshold to -644, size is
6651900(previously 6543232) ...</div>
<div>Increasing upper threshold to -580, size is
6731677(previously 6651900) ...</div>
<div>Increasing upper threshold to -516, size is
6796423(previously 6731677) ...</div>
<div>Increasing upper threshold to -452, size is
6852266(previously 6796423) ...</div>
<div>Increasing upper threshold to -388, size is
6903576(previously 6852266) ...</div>
<div>Increasing upper threshold to -324, size is
6953100(previously 6903576) ...</div>
<div>Increasing upper threshold to -260, size is
7002715(previously 6953100) ...</div>
<div>No explosion before maximum upper threshold reached!</div>
<div>Initial region size using thresholds [-2000, -900], is
4134619...</div>
<div>Increasing upper threshold to -836, size is
5983512(previously 4134619) ...</div>
<div>Increasing upper threshold to -772, size is
6367804(previously 5983512) ...</div>
<div>Increasing upper threshold to -708, size is
6543232(previously 6367804) ...</div>
<div>Increasing upper threshold to -644, size is
6651900(previously 6543232) ...</div>
<div>Increasing upper threshold to -580, size is
6731677(previously 6651900) ...</div>
<div>Increasing upper threshold to -516, size is
6796423(previously 6731677) ...</div>
<div>Increasing upper threshold to -452, size is
6852266(previously 6796423) ...</div>
<div>Increasing upper threshold to -388, size is
6903576(previously 6852266) ...</div>
<div>Increasing upper threshold to -324, size is
6953100(previously 6903576) ...</div>
<div>Increasing upper threshold to -260, size is
7002715(previously 6953100) ...</div>
<div>No explosion before maximum upper threshold reached!</div>
<div>Initial region size using thresholds [-2000, -900], is
4134458...</div>
<div>Increasing upper threshold to -836, size is
5983512(previously 4134458) ...</div>
<div>Increasing upper threshold to -772, size is
6367804(previously 5983512) ...</div>
<div>Increasing upper threshold to -708, size is
6543232(previously 6367804) ...</div>
<div>Increasing upper threshold to -644, size is
6651900(previously 6543232) ...</div>
<div>Increasing upper threshold to -580, size is
6731677(previously 6651900) ...</div>
<div>Increasing upper threshold to -516, size is
6796423(previously 6731677) ...</div>
<div>Increasing upper threshold to -452, size is
6852266(previously 6796423) ...</div>
<div>Increasing upper threshold to -388, size is
6903576(previously 6852266) ...</div>
<div>Increasing upper threshold to -324, size is
6953100(previously 6903576) ...</div>
<div>Increasing upper threshold to -260, size is
7002715(previously 6953100) ...</div>
<div>No explosion before maximum upper threshold reached!</div>
<div>Initial region size using thresholds [-2000, -900], is
4133592...</div>
<div>Increasing upper threshold to -836, size is
5983512(previously 4133592) ...</div>
<div>Increasing upper threshold to -772, size is
6367804(previously 5983512) ...</div>
<div>Increasing upper threshold to -708, size is
6543232(previously 6367804) ...</div>
<div>Increasing upper threshold to -644, size is
6651900(previously 6543232) ...</div>
<div>Increasing upper threshold to -580, size is
6731677(previously 6651900) ...</div>
<div>Increasing upper threshold to -516, size is
6796423(previously 6731677) ...</div>
<div>Increasing upper threshold to -452, size is
6852266(previously 6796423) ...</div>
<div>Increasing upper threshold to -388, size is
6903576(previously 6852266) ...</div>
<div>Increasing upper threshold to -324, size is
6953100(previously 6903576) ...</div>
<div>Increasing upper threshold to -260, size is
7002715(previously 6953100) ...</div>
<div>No explosion before maximum upper threshold reached!</div>
<div>Initial region size using thresholds [-2000, -900], is
4133078...</div>
<div>Increasing upper threshold to -836, size is
5983518(previously 4133078) ...</div>
<div>Increasing upper threshold to -772, size is
6367804(previously 5983518) ...</div>
<div>Increasing upper threshold to -708, size is
6543232(previously 6367804) ...</div>
<div>Increasing upper threshold to -644, size is
6651900(previously 6543232) ...</div>
<div>Increasing upper threshold to -580, size is
6731677(previously 6651900) ...</div>
<div>Increasing upper threshold to -516, size is
6796423(previously 6731677) ...</div>
<div>Increasing upper threshold to -452, size is
6852266(previously 6796423) ...</div>
<div>Increasing upper threshold to -388, size is
6903576(previously 6852266) ...</div>
<div>Increasing upper threshold to -324, size is
6953100(previously 6903576) ...</div>
<div>Increasing upper threshold to -260, size is
7002715(previously 6953100) ...</div>
<div>No explosion before maximum upper threshold reached!</div>
<div>Initial region size using thresholds [-2000, -900], is
4132234...</div>
<div>Increasing upper threshold to -836, size is
5983517(previously 4132234) ...</div>
<div>Increasing upper threshold to -772, size is
6367804(previously 5983517) ...</div>
<div>Increasing upper threshold to -708, size is
6543232(previously 6367804) ...</div>
<div>Increasing upper threshold to -644, size is
6651900(previously 6543232) ...</div>
<div>Increasing upper threshold to -580, size is
6731677(previously 6651900) ...</div>
<div>Increasing upper threshold to -516, size is
6796423(previously 6731677) ...</div>
<div>Increasing upper threshold to -452, size is
6852266(previously 6796423) ...</div>
<div>Increasing upper threshold to -388, size is
6903576(previously 6852266) ...</div>
<div>Increasing upper threshold to -324, size is
6953100(previously 6903576) ...</div>
<div>Increasing upper threshold to -260, size is
7002715(previously 6953100) ...</div>
<div>No explosion before maximum upper threshold reached!</div>
<div>Initial region size using thresholds [-2000, -900], is
4132508...</div>
<div>Increasing upper threshold to -836, size is
5983536(previously 4132508) ...</div>
<div>Increasing upper threshold to -772, size is
6367804(previously 5983536) ...</div>
<div>Increasing upper threshold to -708, size is
6543232(previously 6367804) ...</div>
<div>Increasing upper threshold to -644, size is
6651900(previously 6543232) ...</div>
<div>Increasing upper threshold to -580, size is
6731677(previously 6651900) ...</div>
<div>Increasing upper threshold to -516, size is
6796423(previously 6731677) ...</div>
<div>Increasing upper threshold to -452, size is
6852266(previously 6796423) ...</div>
<div>Increasing upper threshold to -388, size is
6903576(previously 6852266) ...</div>
<div>Increasing upper threshold to -324, size is
6953100(previously 6903576) ...</div>
<div>Increasing upper threshold to -260, size is
7002715(previously 6953100) ...</div>
<div>No explosion before maximum upper threshold reached!</div>
<div>Initial region size using thresholds [-2000, -900], is
4132452...</div>
<div>Increasing upper threshold to -836, size is
5983514(previously 4132452) ...</div>
<div>Increasing upper threshold to -772, size is
6367804(previously 5983514) ...</div>
<div>Increasing upper threshold to -708, size is
6543232(previously 6367804) ...</div>
<div>Increasing upper threshold to -644, size is
6651900(previously 6543232) ...</div>
<div>Increasing upper threshold to -580, size is
6731677(previously 6651900) ...</div>
<div>Increasing upper threshold to -516, size is
6796423(previously 6731677) ...</div>
<div>Increasing upper threshold to -452, size is
6852266(previously 6796423) ...</div>
<div>Increasing upper threshold to -388, size is
6903576(previously 6852266) ...</div>
<div>Increasing upper threshold to -324, size is
6953100(previously 6903576) ...</div>
<div>Increasing upper threshold to -260, size is
7002715(previously 6953100) ...</div>
<div>No explosion before maximum upper threshold reached!</div>
<div>Initial region size using thresholds [-2000, -900], is
4132529...</div>
<div>Increasing upper threshold to -836, size is
5983584(previously 4132529) ...</div>
<div>Increasing upper threshold to -772, size is
6367832(previously 5983584) ...</div>
<div>Increasing upper threshold to -708, size is
6543243(previously 6367832) ...</div>
<div>Increasing upper threshold to -644, size is
6651915(previously 6543243) ...</div>
<div>Increasing upper threshold to -580, size is
6731693(previously 6651915) ...</div>
<div>Increasing upper threshold to -516, size is
6796446(previously 6731693) ...</div>
<div>Increasing upper threshold to -452, size is
6852292(previously 6796446) ...</div>
<div>Increasing upper threshold to -388, size is
6903607(previously 6852292) ...</div>
<div>Increasing upper threshold to -324, size is
6953136(previously 6903607) ...</div>
<div>Increasing upper threshold to -260, size is
7002764(previously 6953136) ...</div>
<div>No explosion before maximum upper threshold reached!</div>
<div>Initial region size using thresholds [-2000, -900], is
4132696...</div>
<div>Increasing upper threshold to -836, size is
5983512(previously 4132696) ...</div>
<div>Increasing upper threshold to -772, size is
6367804(previously 5983512) ...</div>
<div>Increasing upper threshold to -708, size is
6543232(previously 6367804) ...</div>
<div>Increasing upper threshold to -644, size is
6651900(previously 6543232) ...</div>
<div>Increasing upper threshold to -580, size is
6731677(previously 6651900) ...</div>
<div>Increasing upper threshold to -516, size is
6796423(previously 6731677) ...</div>
<div>Increasing upper threshold to -452, size is
6852266(previously 6796423) ...</div>
<div>Increasing upper threshold to -388, size is
6903576(previously 6852266) ...</div>
<div>Increasing upper threshold to -324, size is
6953100(previously 6903576) ...</div>
<div>Increasing upper threshold to -260, size is
7002715(previously 6953100) ...</div>
<div>No explosion before maximum upper threshold reached!</div>
<div>Initial region size using thresholds [-2000, -900], is
4132831...</div>
<div>Increasing upper threshold to -836, size is
5983556(previously 4132831) ...</div>
<div>Increasing upper threshold to -772, size is
6367804(previously 5983556) ...</div>
<div>Increasing upper threshold to -708, size is
6543232(previously 6367804) ...</div>
<div>Increasing upper threshold to -644, size is
6651900(previously 6543232) ...</div>
<div>Increasing upper threshold to -580, size is
6731677(previously 6651900) ...</div>
<div>Increasing upper threshold to -516, size is
6796423(previously 6731677) ...</div>
<div>Increasing upper threshold to -452, size is
6852266(previously 6796423) ...</div>
<div>Increasing upper threshold to -388, size is
6903576(previously 6852266) ...</div>
<div>Increasing upper threshold to -324, size is
6953100(previously 6903576) ...</div>
<div>Increasing upper threshold to -260, size is
7002715(previously 6953100) ...</div>
<div>No explosion before maximum upper threshold reached!</div>
<div>Initial region size using thresholds [-2000, -900], is
4133404...</div>
<div>Increasing upper threshold to -836, size is
5983569(previously 4133404) ...</div>
<div>Increasing upper threshold to -772, size is
6367820(previously 5983569) ...</div>
<div>Increasing upper threshold to -708, size is
6543232(previously 6367820) ...</div>
<div>Increasing upper threshold to -644, size is
6651900(previously 6543232) ...</div>
<div>Increasing upper threshold to -580, size is
6731677(previously 6651900) ...</div>
<div>Increasing upper threshold to -516, size is
6796423(previously 6731677) ...</div>
<div>Increasing upper threshold to -452, size is
6852266(previously 6796423) ...</div>
<div>Increasing upper threshold to -388, size is
6903576(previously 6852266) ...</div>
<div>Increasing upper threshold to -324, size is
6953100(previously 6903576) ...</div>
<div>Increasing upper threshold to -260, size is
7002715(previously 6953100) ...</div>
<div>No explosion before maximum upper threshold reached!</div>
<div>Initial region size using thresholds [-2000, -900], is
4133715...</div>
<div>Increasing upper threshold to -836, size is
5983572(previously 4133715) ...</div>
<div>Increasing upper threshold to -772, size is
6367804(previously 5983572) ...</div>
<div>Increasing upper threshold to -708, size is
6543232(previously 6367804) ...</div>
<div>Increasing upper threshold to -644, size is
6651900(previously 6543232) ...</div>
<div>Increasing upper threshold to -580, size is
6731677(previously 6651900) ...</div>
<div>Increasing upper threshold to -516, size is
6796423(previously 6731677) ...</div>
<div>Increasing upper threshold to -452, size is
6852266(previously 6796423) ...</div>
<div>Increasing upper threshold to -388, size is
6903576(previously 6852266) ...</div>
<div>Increasing upper threshold to -324, size is
6953100(previously 6903576) ...</div>
<div>Increasing upper threshold to -260, size is
7002715(previously 6953100) ...</div>
<div>No explosion before maximum upper threshold reached!</div>
<div>2 : Number of slices to skip to find trachea too high =
65</div>
<div><br>
</div>
<div>itk::ExceptionObject (0x280e930)</div>
<div>Location: "Unknown" </div>
<div>File:
/home/md1bat/Source/vv/segmentation/clitkExtractLungFilter.txx</div>
<div>Line: 266</div>
<div>Description: No seeds for trachea... Aborting.</div>
<div><br>
</div>
<div><br>
</div>
<div><br>
</div>
</div>
</div>
</div>
<div class="gmail_extra">
<br>
<br>
<div class="gmail_quote">On 23 October 2013 22:38, 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"> 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
<div>
<div class="h5"><br>
<br>
<div>On 23/10/2013 19:20, Bilal Tahir wrote:<br>
</div>
<blockquote 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>
<table
style="font-family:arial,sans-serif;font-size:12.727272033691406px"
cellpadding="0">
<tbody>
<tr>
<td 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
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><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>
_______________________________________________<br>
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<a moz-do-not-send="true"
href="mailto:vv@creatis.insa-lyon.fr" target="_blank">vv@creatis.insa-lyon.fr</a><br>
<a moz-do-not-send="true"
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>_______________________________________________
vv mailing list
<a moz-do-not-send="true" href="mailto:vv@creatis.insa-lyon.fr" target="_blank">vv@creatis.insa-lyon.fr</a>
<a moz-do-not-send="true" href="http://www.creatis.insa-lyon.fr/mailman/listinfo/vv" target="_blank">http://www.creatis.insa-lyon.fr/mailman/listinfo/vv</a>
</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>
<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>
<br>
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