[Insight-users] N4ITK running error

[Nicholas Tustison]

Hi Shandra,

There are people on the list that could give a much more
complete and formal answer as to why you don’t do processing
using dicom images.  I’ll simply defer to them and say that
you should use one of the more standard medical imaging
formats that ITK supports like nifti or nrrd or mhd.

Nick 



On Jan 31, 2014, at 9:35 AM, Shandra Gutierrez Diaz <Shandra.GutierrezDiaz at UGent.be> wrote:

> 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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> 

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