[Vv] Errors with clitkExtractLung
Rômulo Pinho
romulopinho at yahoo.com.br
Wed Oct 23 23:38:08 CEST 2013
Ok, Bilal, thanks for the update.
It's hard for me to check it now, because I'd have to download/compile
the entire VV project plus ITK, VTK, etc.
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.
Best,
Rômulo
On 23/10/2013 19:20, Bilal Tahir wrote:
> 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
> <mailto: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
>> <mailto: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
>>
>> _______________________________________________
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>>
>>
>>
>>
>> --
>> Bilal Tahir,
>> James Morrison Researcher in Radiotherapy Imaging,
>> Department of Clinical Oncology,
>> University of Sheffield
>>
>>
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>> vv at creatis.insa-lyon.fr <mailto: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
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