[Insight-developers] N4 in ITK

Hans Johnson hans-johnson at uiowa.edu
Fri Dec 10 17:35:33 EST 2010 

Nick,

I think your plan is perfect!

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: Fri, 10 Dec 2010 11:22:03 -0500
> To: Luis Ibanez <luis.ibanez at kitware.com>
> Cc: Kent Williams <norman-k-williams at uiowa.edu>, Hans Johnson
> <hans-johnson at uiowa.edu>, ITK <insight-developers at itk.org>
> Subject: Re: [Insight-developers] N4 in ITK
> 
> Hi Luis,
> 
> Thanks.  With Richard's changes, the code should be in really good shape.
> Regarding what files to include, unless anybody else objects, I was just
> planning on putting in
> 
> itkBSplineControlPointImageFilter.h, .txx
> itkN4MRIBiasFieldCorrectionImageFilter.h, .txx
> 
> the itkN3* files were an early incarnation of the work trying to mimic the
> actual N3 developed at MNI.  It was during that development that I thought a
> couple changes to the original algorithm would improve things thus yielding
> N4.  
> 
> While I don't worry about the proper credit, it would be a really nice
> exercise in using the gerrit system.  I'll start working on that.
> 
> Thanks,
> Nick 
> 
> 
> On Dec 10, 2010, at 10:52 AM, Luis Ibanez wrote:
> 
>> Hi Nick,
>> 
>> Moving the source code into Review seems to be the way to go.
>> 
>> Just to double check:
>> 
>> We are talking about:
>> 
>> http://www.insight-journal.org/browse/publication/640
>> 
>> and the files that should be moved are:
>> 
>> itkBSplineControlPointImageFilter.h
>> itkBSplineControlPointImageFilter.txx
>> itkN3MRIBiasFieldCorrectionImageFilter.h
>> itkN3MRIBiasFieldCorrectionImageFilterTest.cxx
>> itkN3MRIBiasFieldCorrectionImageFilter.txx
>> itkN4MRIBiasFieldCorrectionImageFilter.h
>> itkN4MRIBiasFieldCorrectionImageFilter.txx
>> 
>> 
>> Is that right ?
>> 
>> 
>> Given that you are the author, you should have the honor
>> of moving the code into ITK, and get the credit for it.
>> 
>> Now that we have git we can better differentiate between
>> authors and committers.
>> 
>> 
>> Would you mind preparing a branch (with
>> its tests) and submitting it to Gerrit ?
>> 
>> 
>> The data may have to go in a separate commit.
>> 
>> 
>>     Thanks
>> 
>> 
>>           Luis
>> 
>> 
>> --------------------------------------------
>> On Wed, Dec 8, 2010 at 2:28 PM, Nicholas Tustison <ntustison at gmail.com>
>> wrote:
>>> Hi Kent,
>>> 
>>> I suspect that on most systems the behavior should be identical.  The issues
>>> addressed by Richard's suggestions were used to correct improper use of the
>>> filter pipelining.  In fact, some were related to the following question you
>>> raised last year on the list:
>>> 
>>> http://www.itk.org/pipermail/insight-users/2009-July/031689.html
>>> 
>>> Hopefully with these changes we can actually minimize the amount of bug
>>> fixes that have to be made once it does get put into ITK and gets tested on
>>> many more systems.
>>> 
>>> Thanks for your help with all this and thanks to Richard for the corrective
>>> suggestions,
>>> Nick
>>> 
>>> 
>>> On Dec 8, 2010, at 2:20 PM, kent williams wrote:
>>> 
>>>> 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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>>>>> 
>>>> 
>>> 
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