[Vv] Errors with clitkExtractLung

Sun Oct 27 22:06:08 CET 2013

On 25 October 2013 14:56, Vivien Delmon
<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,

Bilal

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
Initial region size using thresholds [-2000, -900], is 0...
Increasing upper threshold to -836, size is 0(previously 0) ...
Increasing upper threshold to -772, size is 0(previously 0) ...
Increasing upper threshold to -708, size is 0(previously 0) ...
Increasing upper threshold to -644, size is 0(previously 0) ...
Increasing upper threshold to -580, size is 0(previously 0) ...
Increasing upper threshold to -516, size is 0(previously 0) ...
Increasing upper threshold to -452, size is 0(previously 0) ...
Increasing upper threshold to -388, size is 0(previously 0) ...
Increasing upper threshold to -324, size is 0(previously 0) ...
Increasing upper threshold to -260, size is 0(previously 0) ...
Increasing upper threshold to -196, size is 0(previously 0) ...
Increasing upper threshold to -132, size is 0(previously 0) ...
Increasing upper threshold to -68, size is 0(previously 0) ...
Increasing upper threshold to -4, size is 0(previously 0) ...
Increasing upper threshold to 60, size is 0(previously 0) ...
Increasing upper threshold to 124, size is 0(previously 0) ...
Increasing upper threshold to 188, size is 0(previously 0) ...
Increasing upper threshold to 252, size is 0(previously 0) ...
Increasing upper threshold to 316, size is 0(previously 0) ...
Increasing upper threshold to 380, size is 0(previously 0) ...
Increasing upper threshold to 444, size is 0(previously 0) ...
Increasing upper threshold to 508, size is 0(previously 0) ...
Increasing upper threshold to 572, size is 0(previously 0) ...
Increasing upper threshold to 636, size is 0(previously 0) ...
Increasing upper threshold to 700, size is 0(previously 0) ...
Increasing upper threshold to 764, size is 0(previously 0) ...
Increasing upper threshold to 828, size is 0(previously 0) ...
Increasing upper threshold to 892, size is 0(previously 0) ...
Increasing upper threshold to 956, size is 0(previously 0) ...
Increasing upper threshold to 1020, size is 0(previously 0) ...
Increasing upper threshold to 1084, size is 0(previously 0) ...
Increasing upper threshold to 1148, size is 0(previously 0) ...
Increasing upper threshold to 1212, size is 0(previously 0) ...
Increasing upper threshold to 1276, size is 0(previously 0) ...
Increasing upper threshold to 1340, size is 0(previously 0) ...
Increasing upper threshold to 1404, size is 0(previously 0) ...
Increasing upper threshold to 1468, size is 0(previously 0) ...
Increasing upper threshold to 1532, size is 0(previously 0) ...
Increasing upper threshold to 1596, size is 0(previously 0) ...
Increasing upper threshold to 1660, size is 0(previously 0) ...
Increasing upper threshold to 1724, size is 0(previously 0) ...
Increasing upper threshold to 1788, size is 0(previously 0) ...
Increasing upper threshold to 1852, size is 0(previously 0) ...
Increasing upper threshold to 1916, size is 0(previously 0) ...
Increasing upper threshold to 1980, size is 0(previously 0) ...
Increasing upper threshold to 2044, size is 0(previously 0) ...
Increasing upper threshold to 2108, size is 0(previously 0) ...
Increasing upper threshold to 2172, size is 0(previously 0) ...
Increasing upper threshold to 2236, size is 0(previously 0) ...
Increasing upper threshold to 2300, size is 0(previously 0) ...
Increasing upper threshold to 2364, size is 0(previously 0) ...
Increasing upper threshold to 2428, size is 0(previously 0) ...
Increasing upper threshold to 2492, size is 0(previously 0) ...
Increasing upper threshold to 2556, size is 0(previously 0) ...
Increasing upper threshold to 2620, size is 0(previously 0) ...
Increasing upper threshold to 2684, size is 0(previously 0) ...

>
> The trachea finding part is not very robust. That's why we tried to fix it
> during LOLA11 challenge. My current version of clitkExtractLung does not
> work with --type=1 I will try to fix it next week to see what happens.
>
>
> --
> Vivien Delmon
> PhD student at CREATIS, Lyon
> Supported by ANRT and ELEKTA
> http://www.creatis.insa-lyon.**fr/rio<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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