[Vv] Errors with clitkExtractLung

[Bilal Tahir]

Thanks Vivien,

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.

1) LOLA 11:

[md1bat at testnode02 mhd]$ clitkExtractLung --verboseStep 1 -i copd1_00.mhd
-a default.afdb -o 00_lungs.mhd --type=1
Step 1 -- Copy and crop input image to 'patient' extends
Step 2 -- Set background to initial image
Step 3 -- Remove Air
Step 4 -- Search for the trachea

itk::InvalidRequestedRegionError (0x2bca660)
Location: "unknown"
File: /home/md1bat/Source/itk/Modules/Core/Common/src/itkDataObject.cxx
Line: 411
Description: Requested region is (at least partially) outside the largest
possible region.

2) Original (type=0)

[md1bat at testnode02 mhd]$ clitkExtractLung --verboseStep 1 -i copd1_00.mhd
-a default.afdb -o 00_lungs.mhd --type=0
Step 1 -- Copy and crop input image to 'patient' extends
Step 2 -- Set background to initial image
Step 3 -- Remove Air
Step 4 -- Search for the trachea
         The volume of the trachea (4035.53 cc) seems not correct. I skip
some slices (0) and restart to find seeds.
         The volume of the trachea (4037.01 cc) seems not correct. I skip
some slices (5) and restart to find seeds.
         The volume of the trachea (4036.86 cc) seems not correct. I skip
some slices (10) and restart to find seeds.
         The volume of the trachea (4036.39 cc) seems not correct. I skip
some slices (15) and restart to find seeds.
         The volume of the trachea (4036.07 cc) seems not correct. I skip
some slices (20) and restart to find seeds.
         The volume of the trachea (4035.31 cc) seems not correct. I skip
some slices (25) and restart to find seeds.
         The volume of the trachea (4035.54 cc) seems not correct. I skip
some slices (30) and restart to find seeds.
         The volume of the trachea (4035.49 cc) seems not correct. I skip
some slices (35) and restart to find seeds.
         The volume of the trachea (4035.39 cc) seems not correct. I skip
some slices (40) and restart to find seeds.
         The volume of the trachea (4035.57 cc) seems not correct. I skip
some slices (45) and restart to find seeds.
         The volume of the trachea (4035.69 cc) seems not correct. I skip
some slices (50) and restart to find seeds.
         The volume of the trachea (4036.09 cc) seems not correct. I skip
some slices (55) and restart to find seeds.
         The volume of the trachea (4036.34 cc) seems not correct. I skip
some slices (60) and restart to find seeds.
2 : Number of slices to skip to find trachea too high = 65

itk::ExceptionObject (0x377f970)
Location: "Unknown"
File: /home/md1bat/Source/vv/segmentation/clitkExtractLungFilter.txx
Line: 266
Description: No seeds for trachea... Aborting.

3) Manually setting a higher number of slices than 65

[md1bat at testnode02 mhd]$ clitkExtractLung --verbose 1 -i copd1_00.mhd -a
default.afdb -o 00_lungs.mhd --skipslices=90
Input is 3D short.
Reading [copd1_00.mhd] ...
2 : Number of slices to skip to find trachea too high = 95

itk::ExceptionObject (0x3a379d0)
Location: "Unknown"
File: /home/md1bat/Source/vv/segmentation/clitkExtractLungFilter.txx
Line: 266
Description: No seeds for trachea... Aborting.

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.

Best wishes,

Bilal


On 23 October 2013 16:51, Vivien Delmon
<vivien.delmon at creatis.insa-lyon.fr>wrote:

> On 10/18/2013 12:08 AM, Bilal Tahir wrote:
>
>> Dear VV community,
>>
>> ...
>>
>>
>> Also I would like to know if the LOLA11 paper below is the correct
>> reference if I decide to use your method for publications?
>>
>> http://lola11.com/Results/**displayApproved?result=**
>> 20110708160218_86_CREATIS_CLB_**Lyon_graphcut&file=**
>> 20110708160218_86_CREATIS_CLB_**Lyon_graphcut_lola11.pdf<http://lola11.com/Results/displayApproved?result=20110708160218_86_CREATIS_CLB_Lyon_graphcut&file=20110708160218_86_CREATIS_CLB_Lyon_graphcut_lola11.pdf>
>>
>
> Part of the work presented in this paper have been implemented in
> clitkExtractLung but you need to explicitly ask the tool to use it :
>
> Step 2 : find trachea:
>   --type=INT trachea finding algorithm (0: original; 1:LOLA11)
> (default=`0')
>
> The second part about graphcut labeling were not included in this tool
> since we never really need to separate lungs.
>
> Last time I tried to activate --type=1 it failed, I will have a look at it
> one day.
>
> 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.
>
> --
> Vivien Delmon
> PhD student at CREATIS, Lyon
> Supported by ANRT and ELEKTA
> http://www.creatis.insa-lyon.**fr/rio<http://www.creatis.insa-lyon.fr/rio>
>
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>



-- 
Bilal Tahir,
James Morrison Researcher in Radiotherapy Imaging,
Department of Clinical Oncology,
University of Sheffield
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