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

Sat Nov 15 07:54:44 EST 2008

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=31
78

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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>> >
> 

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