[Insight-users] N4ITK running error

[Shandra Gutierrez Diaz]

Hi Nick, 

I have tried the ANTs version and it works properly with the examples. However when I am trying to do it with my images (dicoms) it doesn't seem to work. It generates a dicom image but it is empty. 
Is it possible to use it with dicom images or should it be nifti?

Shandra

On 30/01/2014, at 15:30, Shandra Gutierrez Diaz wrote:

> Hi Nick,
> 
> Thanks a lot for the feedback. I thought I was doing something wrong. I will try then with the ANTS version. 
> 
> Best, 
> Shandra
> On 30/01/2014, at 15:26, Nicholas Tustison wrote:
> 
>> Hi Shandra,
>> 
>> I tried downloading the IJ code and it no longer works
>> with the current ITK because of the numerous changes
>> made to the core classes.  The only N4 program that I 
>> continue to maintain is the ANTs version 
>> 
>> http://stnava.github.io/ANTs/
>> 
>> The program, N4.cxx, evolved into N4BiasFieldCorrection.cxx
>> 
>> https://github.com/stnava/ANTs/blob/master/Examples/N4BiasFieldCorrection.cxx
>> 
>> and I can run it just fine using your command line.
>> 
>> [ntustison at d-172-25-171-144 Thu Jan 30 09:15:24] $ N4BiasFieldCorrection -d  2 -i t81slice.nii.gz -o t81sliceCorrect.nii.gz -s 4 -b [200] -c [50x50x50x50,0]
>> 
>> Running N4 for 2-dimensional images.
>> 
>> Mask not read.  Creating Otsu mask.
>> Current level = 1
>>   Iteration 1 (of 50).   Current convergence value = 0.000515799 (threshold = 0)
>>   Iteration 2 (of 50).   Current convergence value = 0.000514015 (threshold = 0)
>>   Iteration 3 (of 50).   Current convergence value = 0.000512207 (threshold = 0)
>>   Iteration 4 (of 50).   Current convergence value = 0.000510627 (threshold = 0)
>>   Iteration 5 (of 50).   Current convergence value = 0.000508918 (threshold = 0)
>>   Iteration 6 (of 50).   Current convergence value = 0.000507124 (threshold = 0)
>>   Iteration 7 (of 50).   Current convergence value = 0.000505515 (threshold = 0)
>>   Iteration 8 (of 50).   Current convergence value = 0.000503797 (threshold = 0)
>>   Iteration 9 (of 50).   Current convergence value = 0.000502342 (threshold = 0)
>>   Iteration 10 (of 50).   Current convergence value = 0.000500771 (threshold = 0)
>>   Iteration 11 (of 50).   Current convergence value = 0.000499355 (threshold = 0)
>>   Iteration 12 (of 50).   Current convergence value = 0.000497954 (threshold = 0)
>>   Iteration 13 (of 50).   Current convergence value = 0.000496292 (threshold = 0)
>>   Iteration 14 (of 50).   Current convergence value = 0.000494926 (threshold = 0)
>>   Iteration 15 (of 50).   Current convergence value = 0.000493357 (threshold = 0)
>>   Iteration 16 (of 50).   Current convergence value = 0.000491692 (threshold = 0)
>> 
>> 
>> Nick
> 
> 
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