[Vv] Errors with clitkExtractLung
Rômulo Pinho
romulopinho at yahoo.com.br
Wed Oct 23 22:41:09 CEST 2013
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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