[Vv] Errors with clitkExtractLung

[Vivien Delmon]

On 11/04/2013 11:02 AM, Vivien Delmon wrote:
> On 10/30/2013 02:58 PM, Bilal Tahir wrote:
>> Hi Vivien,
>>
>> I tried exactly your two commands and saved the output in a file in the
>> link below with the verbose RG option. I set the script to terminate
>> after 7 hours.
>>
>> https://www.dropbox.com/s/z6e0byux2qftn73/lungmask.o7302811
>>
>> As you  can see, even after 7 hours, it still gives the 'size is 0'
>> message. I haven't updated clitk for a few months. I guess this means
>> that there were some recent patches in the last few months?
>
> Hi Bilal,
>
> On my computer it takes 1 or 2 minutes so you have a problem ... The log
> says that the region growing obtain 0 voxels with the threshold used.
> It's quite strange did you checked that the values are in Hounsfield
> units ?
>
> I will have a look at the data I gave you, probably this afternoon. i
> don't think that they have been lot of changes in clitkExtractLungs so
> it's definitely strange.
>

Hi Bilal,

You mention that you have an old version of clitkExtractLung and it 
remind me that some month ago (1 July) we change the --seed option that 
was taking coordinates in voxel to use physical coordinates.

So you should try :

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 
240,200,113

150,125,-18 mm^3 = 240,200,113 voxel^3

Kind regards,

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