[ITK] Regularizing b-spline deformation in ITKv4

[Andriy Fedorov]

Stefan,

didn't know about SimpleElastix, but I am well-aware of the elastix powers!

This solution is not ideal for us, since elastix is not integrated
with 3D Slicer, and also if I recall correctly, the format used by
elastix for deformable transforms is not the same as the one used by
ITK.

It is definitely a good idea to compare other deformable registration
tools, but I was just wondering if there is a regularization in ITKv4
we can add to the Slicer/ITKv4 registration tool already integrated
into our workflows.

>From the responses I am getting so far, it looks like the answer is
either "no" or adding such regularization is not straightforward.

AF

On Wed, May 20, 2015 at 6:35 PM, S. Klein <s.klein at erasmusmc.nl> wrote:
> Hi Andriy,
>
> Not sure if it is what you are looking for, but you could also try SimpleElastix:
> https://github.com/kaspermarstal/SimpleElastix
> It builds with ITK v4, and is based on simpleITK.  It includes B-spline registration with plenty of options for tuning (perhaps too many ;) )
>
> Best,
> Stefan
> ________________________________________
> From: Community [community-bounces at itk.org] on behalf of Andriy Fedorov [fedorov at bwh.harvard.edu]
> Sent: Wednesday, May 20, 2015 23:08
> To: Nicholas Tustison
> Cc: Community at itk.org; ITK Users
> Subject: Re: [ITK] Regularizing b-spline deformation in ITKv4
>
> Nick,
>
> we are comparing BRAINSFit in Slicer3 that was based on ITKv3 vs
> BRAINSFit in Slicer4 based on ITKv4.
>
> We have been using BRAINSFit/Slicer3 for a long time on a large number
> of clinical research cases and we've been reasonably happy with the
> results.
>
> We need something that is integrated in Slicer, or can be implemented
> in SimpleITK relatively easily. We need a tool that produces a
> reasonable result within 2 minutes of computation, without the need to
> change parameters depending on the dataset. So these are basically our
> constraints. We were hoping we could improve BRAINSFit/Slicer4 by
> adding a regularizer, or implement a subset of BRAINSFit functionality
> in SimpleITK.
>
> AF
>
> On Wed, May 20, 2015 at 11:39 AM, Nicholas Tustison <ntustison at gmail.com> wrote:
>> Hi Andriy,
>>
>> How are you comparing ITKv3 with ITKv4?  I assume you’re running
>> ITKv3 through BRAINSFit but how are you running ITKv4?
>>
>> There are a couple of alternative B-spline methods if you’re interested.
>> There’s B-spline SyN which is described here
>>
>> http://www.ncbi.nlm.nih.gov/pubmed/24409140
>>
>> and
>>
>> a Demon’s like B-spline algorithm described here
>>
>> http://www.ncbi.nlm.nih.gov/pubmed/19171516
>>
>> which both offer different regularization options that are available in
>> ITKv4.  However, alternative explicit regularization models, such as
>> thin plate splines, are not available in ITKv4.
>>
>> Nick
>>
>>
>>
>>
>>
>> On May 19, 2015, at 5:38 PM, Andriy Fedorov <fedorov at bwh.harvard.edu> wrote:
>>
>> Hi,
>>
>> we are in the process of evaluating the possibility of migrating
>> workflows from ITKv3 to ITKv4 b-spline based registration (see details
>> here [1]).
>>
>> One issue that is becoming apparent is that sometime the deformations
>> we are getting with ITKv4 lack are a lot more irregular and
>> unrealistic than what we used to get in ITKv3 (see case 9 on the page
>> referenced).
>>
>> At the ITK community hangout last week it was suggested that there are
>> some ways in ITKv4 to add regularization to b-spline transformation.
>>
>> Is there an example of b-spline regularization we could follow to see
>> how this should be done? Is there a significant performance hit if
>> this regularization is used?
>>
>> Thanks
>>
>> AF
>>
>> [1] http://www.na-mic.org/Wiki/index.php/BRAINSFit_prostate_registration
>>
>>
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