[Insight-developers] N4 in ITK

[kent williams]

I just downloaded the IJ article again, and copied in the
itkN4MRIBiasFieldCorrectionImageFilter.(txx,h) into our BRAINS3 tree.
Looking at a diff, I don't see huge changes, so I'll have to take your word
for it that you've improved it.

I'm not close enough to the code to know how 'ITK-ready' it is. I do know
that we do use it at Iowa as part of our 'standard workup' for brain images.

I do know that you do include tests and some reasonably compact test images.
If there's concensus to move the N4 class into ITK, it could go in pretty
easily.


On 12/8/10 11:56 AM, "Nicholas Tustison" <ntustison at gmail.com> wrote:

> Hi Kent,
> 
> The N4 contribution has been updated on the IJ with Richard's suggestions.
> Everything seems to run properly on my two mac machines and all the IJ tests
> continue to pass but, since I can't test other platforms, please let me know
> if you run into any difficulties the next time you sync.
> 
> Thanks,
> Nick
> 
> 
> On Dec 7, 2010, at 11:39 AM, Hans Johnson wrote:
> 
>> Nick,
>> 
>> I'd support putting the general ITK process objects that have wider usage
>> into ITK, and putting the application that is used into Slicer3.  Let the
>> ITK community maintain the core algorithmic pieces, and the Slicer community
>> maintain the end user application interfaces.
>> 
>> Hans
>> 
>> -- 
>> Hans J. Johnson, Ph.D.
>> Hans-johnson at uiowa.edu
>> 
>> 278 GH
>> The University of Iowa
>> Iowa City, IA 52241
>> (319) 353 8587
>> 
>> 
>>> From: Nicholas Tustison <ntustison at gmail.com>
>>> Date: Tue, 7 Dec 2010 10:40:06 -0500
>>> To: Kent Williams <norman-k-williams at uiowa.edu>
>>> Cc: ITK <insight-developers at itk.org>, Luis Ibanez <luis.ibanez at kitware.com>
>>> Subject: Re: [Insight-developers] N4 in ITK
>>> 
>>> Hi Kent,
>>> 
>>> That's what I had figured that you all were heavy users/testers like we are
>>> at
>>> Penn.  In addition, Andriy interfaces with the slicer community regarding
>>> N4.
>>> And as far as I know, nobody has ran into any issues until recently when
>>> Richard had problems with his set up.  What would be nice (and I say this
>>> because I'm completely lazy) is to simply pass ownership to the ITK
>>> community
>>> where these issues would be better addressed via the Dashboard versus me
>>> making changes to N4 through the IJ and hoping that I don't break anybody
>>> else's set-up with the changes.
>>> 
>>> Nick
>>> 
>>> 
>>> 
>>> 
>>> On Dec 7, 2010, at 10:20 AM, kent williams wrote:
>>> 
>>>> We try and keep in sync in the BRAINS3 project and have a regular dashboard
>>>> build. We also have several tests we run.
>>>> 
>>>> 
>>>> On 12/7/10 8:13 AM, "Nicholas Tustison" <ntustison at gmail.com> wrote:
>>>> 
>>>>> Hi Luis,
>>>>> 
>>>>> Richard Beare ran into a couple issues running N4 recently on a couple of
>>>>> his
>>>>> systems which I hadn't encountered.  He worked out a solution which I plan
>>>>> to
>>>>> propagate back to the IJ as a revision soon.  However, considering the
>>>>> number
>>>>> of people that actually use the code and the fact that addressing these
>>>>> issues
>>>>> would be better done in a versioning/review system where I can actually
>>>>> see
>>>>> the results from these subtle code changes on different systems on the
>>>>> dashboard, is there a mechanism that would allow for inclusion of new code
>>>>> into itkv4 even amidst all the *chaos that is the current itkv4
>>>>> development
>>>>> process?  However, I certainly don't want to seem like I'm trying to force
>>>>> in
>>>>> my own code into the repository.
>>>>> 
>>>>> Nick
>>>>> 
>>>>> *(I use the term "chaos" only for rhetorical effect and I actually
>>>>> appreciate
>>>>> all the work that's been done to make it as smooth as it has been.)
>>>>> 
>>>>> 
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>