[Vv] Errors with clitkExtractLung

[David Sarrut]

Hello Bilal,

I know this is not optimal, but currently, the clitkExtractLung need a
previous segmentation of the patient contour. It can be obtained with
clitkExtractPatient first. The result is a binary image. The txt file .afdb
just indicates to clitkExtractLung the filename of the patient contour.

So in short : try clitkExtractPatient first, it will create the binary
image + afdb file.

keep us in touch if it is working,
Sincerely,
David


On Wed, Oct 23, 2013 at 5:05 PM, Bilal Tahir <b.tahir at sheffield.ac.uk>wrote:

> Dear VV community,
>
> Going back to my previous errors with running *clitkExtractLung, *I would
> like to know what the .afdb file is and why it is causing errors? I only
> want to create masks for the left and right lungs and not anything else
> such as the trachea/airways so I'm not sure why I am getting this error.
> Perhaps its a mistake in my command line?
>
> Best wishes,
>
> Bilal
>
>
> On 17 October 2013 23:08, Bilal Tahir <b.tahir at sheffield.ac.uk> wrote:
>
>> Dear VV community,
>>
>> I am getting some errors with clitkExtractLung for the COPD dir lab CT
>> datasets. I basically set the input but leave everything else with default
>> values. Here is my output below:
>>
>> [md1bat at testnode04 mhd]$ clitkExtractLung --verbose --input=copd1_00.mhd
>> Input is 3D short.
>> Reading [copd1_00.mhd] ...
>> ******* Could not read 'default.afdb', create one AFDB. ********
>>
>> itk::ExceptionObject (0x23f2da0)
>> Location: "Unknown"
>> File:
>> /home/md1bat/Source/vv/segmentation/clitkAnatomicalFeatureDatabase.txx
>> Line: 27
>> Description: Could not find the tag <Patient> of type 'Image' in the DB
>> ('default.afdb')
>>
>>
>> Please let me know your suggestions?
>>
>> 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
>>
>>
>> Kind regards,
>>
>> Bilal Tahir,
>> James Morrison Researcher in Radiotherapy Imaging,
>> Department of Clinical Oncology,
>> University of Sheffield
>>
>
>
>
> --
> Bilal Tahir,
> James Morrison Researcher in Radiotherapy Imaging,
> Department of Clinical Oncology,
> University of Sheffield
>
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>
>


-- 
David Sarrut, Phd
Directeur de recherche CNRS
CREATIS, UMR CNRS 5220, Inserm U 1044
Centre de lutte contre le cancer Léon Bérard
28 rue Laënnec, 69373 Lyon cedex 08
Tel : 04 78 78 51 51 / 06 74 72 05 42
http://www.creatis.insa-lyon.fr/~dsarrut
_________________________________
 "2 + 2 = 5,  for extremely large values of 2"
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