[Insight-developers] ITK Image orientation fixes with regards to Demons filters

[Tom Vercauteren]

Thank you so much Hans for investigating this. It sounds perfect!

I am currently away from my computer but hope I can soon test a case
where the the Origins, Spacing, Size, and Directions are all different
in each image.

This will definitely ease working with datasets such as brainweb 20
(http://www.bic.mni.mcgill.ca/brainweb/anatomic_normal_20.html) which
required quite a lot of preprocessing to be usable in ITK.

Regards,
Tom

On Sat, Nov 15, 2008 at 1:54 PM, Hans Johnson <hans-johnson at uiowa.edu> wrote:
> Tom,
>
> I wanted to bring to your attention some bug fixes with regards to using ITK
> oriented images and Demons registration.
>
> These were the updates that occurred:
> http://www.cdash.org/CDash/viewUpdate.php?buildid=214181
> To fix this bug:
> http://public.kitware.com/dashboard.php?name=itk
>
> And these changes allowed all tests to pass with regards our
> DemonsRegistration algorithm
> http://testing.psychiatry.uiowa.edu/CDash/viewTest.php?onlypassed&buildid=3178
>
> This can even register 2 data sets where the the Origins, Spacing, Size, and
> Directions are all different in each image.
>
> Hans
>
>
> On 10/21/08 11:33 AM, "Tom Vercauteren" <tom.vercauteren at m4x.org> wrote:
>
> Hi Hans,
>
> Thanks for the heads up! I wasn't aware of that work and it looks
> definitely better than what I was proposing.
>
> As apparently there already is a community working on maintaining and
> improving the demons tools on www.nitrc.org, of course it makes sense
> to keep the development there.
>
> I just hope we can manage to keep the work on the core filters within
> ITK. Then having only a copy of the command-line tools within
> InsightApplications would be fine.
>
> I need to look into the details of BrainDemonsWarp www.nitrc.org to
> see how we can combine things.
>
> Best,
> Tom
>
> On Tue, Oct 21, 2008 at 5:59 PM, Hans Johnson <hans-johnson at uiowa.edu>
> wrote:
>> Tom,
>>
>> Your work on diffeomorphic demons is fabulous.  We have been working hard
>> to
>> incorporate your diffeomorphic work into our existing demons registration
>> application.  We have a version that is compatible with your version at
>> the
>> command line level, but also has some other advantages:  1) Tested each
>> night on multiple platforms to above 70% code coverage, 2) additional
>> documentation to complement your documents, 3) a code dashboard for
>> following managing the development process, 4) It is built with the
>> Slicer3
>> command line execution model, 5) Tested and cleaned up with valgrind, 6)
>> Available and registered with www.nitrc.org.
>>
>>
>> http://testing.psychiatry.uiowa.edu/CDash/index.php?project=BRAINSDemonWarp
>> http://www.nitrc.org/projects/brainsdemonwarp/
>> http://www.nitrc.org/docman/view.php/151/480/BRAINSDemonWarp.pdf
>>
>> I am hoping that we can collaborate to combine our two tools documentation
>> and executables so that we can provide better tools to the registration
>> community.  I agree that making these tools more widely available is a
>> good
>> goal, and I would support including a copy of the tool in
>> InsightApplications, but I would prefer to use www.nitrc.org to manage the
>> development environment surrounding the development process and bug fixes
>> for future versions of the tools.
>>
>> Please let me know you thoughts.
>>
>> Regards,
>> 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: Tom Vercauteren <tom.vercauteren at gmail.com>
>>> Reply-To: <tom.vercauteren at m4x.org>
>>> Date: Tue, 21 Oct 2008 17:31:38 +0200
>>> To: ITK <insight-developers at itk.org>
>>> Subject: [Insight-developers] Policy for adding an application
>>> toInsightApplications
>>>
>>> Hi,
>>>
>>> I am wondering what the policy is for adding new applications to
>>> InsightApplications.
>>>
>>> Now that all the filters from the diffeomorphic demons insight journal
>>> submission have been integrated to ITK, I thought it might be worth
>>> adding the demons command-line tool to InsightApplications.
>>>
>>> The code consists of a single c++ file with some CMake and testing
>>> stuff. It uses metaCommand to parse the command-line arguments and has
>>> a few options as shown below.
>>>
>>> Would there be an interest in committing that to InsightApplications
>>> or to the ITK registration examples?
>>>
>>> Regards,
>>> Tom
>>>
>>> $ ./DemonsRegistration
>>> Option FixedImageFile is required but not defined
>>> Option MovingImageFile is required but not defined
>>>  Command tags:
>>>    -f --fixed-image < filename >
>>>       = Fixed image filename
>>>    -m --moving-image < filename >
>>>       = Moving image filename
>>>    [ -b --input-field < filename > ]
>>>       = Input field filename
>>>    [ -p --input-transform < filename > ]
>>>       = Input transform filename
>>>    [ -o --output-image < filename > ]
>>>       = Output image filename
>>>         With: filename (Default = output.mha)
>>>    [ -O --output-field [ filename ] ]
>>>       = Generate the output field and optionally specify a filename
>>>         With: filename (Default = OUTPUTIMAGENAME-field.mha)
>>>    [ -r --true-field < filename > ]
>>>       = Specify a "true" field to compare the registration result with
>>> (useful for synthetic experiments)
>>>    [ -i --num-iterations < uintvect > ]
>>>       = List of number of iterations for each multi-scale pyramid
>>> level < UINTx...xUINT >
>>>         With: uintvect (Default = 15x10x5)
>>>    [ -s --def-field-sigma < floatval > ]
>>>       = Smoothing sigma for the deformation field (pixel units).
>>> Setting it value below 0.5 means no smoothing will be performed
>>>         With: floatval (Default = 1.5)
>>>    [ -g --up-field-sigma < floatval > ]
>>>       = Smoothing sigma for the update field (pixel units). Setting it
>>> below 0.5 means no smoothing will be performed
>>>         With: floatval (Default = 0.0)
>>>    [ -l --max-step-length < floatval > ]
>>>       = Maximum length of an update vector (pixel units). Setting it
>>> to 0 implies no restrictions will be made on the step length
>>>         With: floatval (Default = 2.0)
>>>    [ -a --update-rule < type > ]
>>>       = Type of update rule. 0: s <- s o exp(u) (diffeomorphic), 1: s
>>> <- s + u (additive, ITK basic), 2: s <- s o (Id+u) (compositive,
>>> Thirion's proposal?)
>>>         With: type (Default = 0)
>>>    [ -t --gradient-type < type > ]
>>>       = Type of gradient used for computing the demons force. 0 is
>>> symmetrized, 1 is fixed image, 2 is warped moving image, 3 is mapped
>>> moving image
>>>         With: type (Default = 0)
>>>    [ -e --use-histogram-matching ]
>>>       = Use histogram matching prior to registration (e.g. for
>>> different MR scanners)
>>>    [ -d --verbose [ intval ] ]
>>>       = Algorithm verbosity (debug level)
>>>         With: intval (Default = 1)
>>> _______________________________________________
>>> Insight-developers mailing list
>>> Insight-developers at itk.org
>>> http://www.itk.org/mailman/listinfo/insight-developers
>>
>>
>>
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