[Vv] Errors with clitkExtractLung

Bilal Tahir b.tahir at sheffield.ac.uk
Wed Oct 23 23:20:15 CEST 2013 

Hi Rômulo,

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.

Best wishes,

Bilal



On 23 October 2013 21:41, Rômulo Pinho <romulopinho at yahoo.com.br> wrote:

>  Hello, Bilal,
>
> 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.
>
> To cope with it, you can either play with the parameters
> seedPreProcessingThreshold and upperThresholdForTrachea in clitkExtratLung
> (depending on TYPE)
> "upperThresholdForTrachea"    -    "0: Initial upper threshold for
> trachea"  default="-900"
> "seedPreProcessingThreshold"   -  "1: Threshold for the pre-processing
> step of the algorithm" default="-400"
>
> 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.
>
> In any case, using --verboseRG might also give some extra insights.
>
> I hope this helps!
>
> Best,
> Rômulo
>
>
> On 23/10/2013 14:15, Bilal Tahir wrote:
>
> 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
>>>
>>
>> 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
>>
>> _______________________________________________
>> vv mailing list
>> vv at creatis.insa-lyon.fr
>> http://www.creatis.insa-lyon.fr/mailman/listinfo/vv
>>
>
>
>
>  --
> Bilal Tahir,
> James Morrison Researcher in Radiotherapy Imaging,
> Department of Clinical Oncology,
> University of Sheffield
>
>
> _______________________________________________
> vv mailing listvv at creatis.insa-lyon.frhttp://www.creatis.insa-lyon.fr/mailman/listinfo/vv
>
>
>


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