[Vv] How can I pass a "patient mask" to clitkExtractLung?

[Vivien Delmon]

On 01/09/2012 05:18 AM, 黄成 wrote:
> Hi all,
>
>           I'm using clitkExtractLung.exe to extract the lung from a CT
> image, and I run it using command line: "clitkExtractLung.exe -i
> myImage.nii"
>           Then I get an error message:
>
> itk::ExceptionObject (00000000009EF4B0)
> Location: "Unknown"
> File: ..\..\..\Source\clitk\common\clitkImageToImageGenericFilterBase.cxx
> Line: 243
> Description: **Error** The filter <ExtractLung> is not available for 3D
> images with pixel=float and 1 component.
> The filter <ExtractLung> manages:
> Dim: 3, Type: short
>
>           Since the help information of clitkExtractLung.exe tells me
> that a patient mask image is needed, I guess I should pass a patient
> mask image as an argument to it. However, I cannot figure out how to do
> this because there is no argument for "patient mask". How can I make
> this work?

Hi Huang,

All clitk tools are developed for internal use and not really adaptable 
to any kind of data. For clitkExtractLung the data file must be encoded 
on signed short using Hounsfield units (-1000 for air).

If your image is in Hounsfield units but the type of data is float you 
can convert it with :
clitkImageConvert -i myImage.nii -o myImage_short.nii -t short

If your image is not scaled on Hounsfield units, scales it using 
clitkImageArithm from which you can add scalar or multiply by scalar or 
anything like this.

For the patient mask clitkExtractLung read a afdb file which is an 
internal format describing a database of patient structures. Its format 
is "<Name of Structure> <path to file>" with one structure on each line 
giving that kind of file :

Lungs tmp.MASK/lungs_0.mhd
Patient tmp.MASK/patient_mask_0.mhd
Trachea trachea.mhd

If you use clitkExtractPatient to obtain the patient mask you can 
specify a afdb file :
clitkExtractPatient -i myImage.nii -o myImage_patient_mask.nii -a 
myImage.afdb

then you can give it to clitkExtractLung :

clitkExtractLung -i myImage_short.nii -a myImage.afdb -o myImage_lungs.nii

I hope this will answer all your questions. Don't hesitate if you have 
more question.

Kind Regards,

-- 
Vivien Delmon
PhD student at CREATIS, Lyon
Supported by ANRT and ELEKTA
http://www.creatis.insa-lyon.fr/rio