[Insight-developers] Policy for adding an application toInsightApplications

Tue Oct 21 12:33:37 EDT 2008

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
>
>
>
> Notice: This UI Health Care e-mail (including attachments) is covered by the Electronic Communications Privacy Act, 18 U.S.C. 2510-2521, is confidential and may be legally privileged.  If you are not the intended recipient, you are hereby notified that any retention, dissemination, distribution, or copying of this communication is strictly prohibited.  Please reply to the sender that you have received the message in error, then delete it.  Thank you.
>
>
>