[Vv] Errors with clitkExtractLung

[Vivien Delmon]

On 10/27/2013 10:06 PM, Bilal Tahir wrote:
> On 25 October 2013 14:56, Vivien Delmon
> <vivien.delmon at creatis.insa-lyon.fr
> <mailto:vivien.delmon at creatis.insa-lyon.fr>> wrote:
>
>     On 10/23/2013 06:15 PM, 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.
>
>
>     For the first patient I successfully got a lung mask by manually
>     giving the seed in the trachea.
>
>     clitkExtractLung -i copd1_50.mhd -o MASK/lungs_mask_copd1_50.mhd
>     --seed 150,125,-18
>
>
>
> Hi Vivien,
>
> Did you use exactly the same command as above for patient copd1_50.mhd?
> I noticed that you didn't add the -a *.afdb option. I tried your command
> as above and with the -a option but I was unable to generate a mask. In
> fact, the program keeps running continuously with a trachea size of 0
> and never seems to terminate. I have copied and pasted a small part of
> the output below but I terminated it after an hour and a half or so.
> Perhaps you added some additional options as Rômulo had suggested?
> Also, I would be very grateful if you could let us know when you have
> fixed the LOLA11 option.
>
> Best wishes,

Hi Bilal,

If you did not give any -a option it uses default.afdb. Which is bad in 
my opinion, since you can call ExtractPatient on 1 image and then 
ExtractLung on another image. In this case the result of ExtractPatient 
on the first image is used to extract the lung of the second patient.

But yes, here I use the fact that this default.afdb were created by a 
previous call to ExtractPatient. I did exactly these 2 commands :

clitkExtractPatient -i copd1_50.mhd -o MASK/patient_mask_copd1_50.mhd
clitkExtractLung -i copd1_50.mhd -o MASK/lungs_mask_copd1_50.mhd --seed 
150,125,-18

The first command create the default.afdb which will be used by the 
second command.

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

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