[Insight-users] Coordinate System of registration-generated displacement field different from systems of inputs??

[Tim Bhatnagar]

Hello again,

I've found this snippet of code on ITK/VTK forums:

FlipFilterType::Pointer flipperImage = FlipFilterType::New();
bool flipAxes[3] = { false, true, false };
flipperImage = FlipFilterType::New();
flipperImage->SetFlipAxes(flipAxes);
flipperImage->SetInput( image );
flipperImage->Update();

Is this an appropriate filter to run my output images (and vector
images) through just before visualization, or will vector images cause
a erroneous results with this?

Thanks again,




On Sat, Oct 12, 2013 at 12:31 PM, Tim Bhatnagar <tim.bhatnagar at gmail.com>wrote:

> Hello all,
>
> Could someone help me understand how the coordinate system of my
> ITK-produced displacement field (from image registration) can be 'flipped
> in the y-direction' to match my input image coordinate systems?
>
> I was pointed to this source:
> http://www.slicer.org/slicerWiki/index.php/Slicer:VTK_ITK_Coordinates ,
> but I'm not sure if that means I should just only flip (ie take the
> negative of) my y-coordinates, or if there are other adjustments that need
> to be made (ie, if I just 'flip' my y-axis, my x-y-z coordinate system will
> no longer be orthogonally correct).
>
> A bit of an explanation would really help. Thank you!
>
>
> On Wed, Oct 9, 2013 at 11:06 AM, Matt McCormick <
> matt.mccormick at kitware.com> wrote:
>
>> Hi Tim,
>>
>> If viewing the data with VTK or other library, deformation in the
>> negative y-direction should be taken with care because of a difference
>> in coordinate systems [1].
>>
>> HTH,
>> Matt
>>
>> [1] http://www.slicer.org/slicerWiki/index.php/Slicer:VTK_ITK_Coordinates
>>
>> On Wed, Oct 9, 2013 at 5:59 PM, Tim Bhatnagar <tim.bhatnagar at gmail.com>
>> wrote:
>> > Thanks Matt,
>> >
>> > It is strange then, that I can extract data from the displacement field
>> that
>> > seems to represent the field that would transform the 'pre-deformation'
>> > image into the 'deformation' image. (There is a significant deformation
>> in
>> > the 'deformation data' in the negative y-direction, which shows up
>> nicely in
>> > the displacement field.
>> >
>> > Must I be doing something strange for this to happen?
>> >
>> >
>> > On Wed, Oct 9, 2013 at 10:31 AM, Matt McCormick <
>> matt.mccormick at kitware.com>
>> > wrote:
>> >>
>> >> Hi Tim,
>> >>
>> >> No, the WarpImageFilter should be generating a 'pre-deformation'
>> >> look-alike.  For more information, see the Software Guide.
>> >>
>> >> HTH,
>> >> Matt
>> >>
>> >> On Wed, Oct 9, 2013 at 4:48 PM, Tim Bhatnagar <tim.bhatnagar at gmail.com
>> >
>> >> wrote:
>> >> > Hello all,
>> >> >
>> >> > I use the ITK examples ImageRegistration5, ImageRegistration8 and
>> >> > DeformableRegistration2 (Demon's) for registration of normal and
>> >> > deformed
>> >> > data (same subject). Briefly, I do some pre-registration of my data
>> >> > using
>> >> > ImageReg5 and ImageReg8 (for gross alignment), after which I take the
>> >> > produced displacement fields, and use them as the 'initial
>> displacement
>> >> > field' for DefReg2.
>> >> >
>> >> > In all cases, I am using my 'pre-deformation' data as my fixed
>> source,
>> >> > and
>> >> > my 'deformation' data as my moving source.
>> >> >
>> >> > I have some fiducial markers to check the accuracy of the generated
>> >> > displacement field, and it looks pretty good. However, when trying to
>> >> > produce figures, my registration output looks much closer to my
>> >> > 'deformation' data, and sometimes the output and the actual
>> >> > 'deformation'
>> >> > data are offset by a magnitude.
>> >> >
>> >> > In my situation, should I be aiming to have my registration output
>> >> > appear
>> >> > similar to my 'pre-deformation' data? (I get confused reading the ITK
>> >> > explanation on that) Shouldn't I be able to produce the a
>> 'deformation'
>> >> > look-a-like by using WarpImageFilter with my 'pre-deformation' data
>> and
>> >> > my
>> >> > generated displacement field?
>> >> >
>> >> > Sorry this was so wordy. Any help would be much appreciated.
>> >> >
>> >> > --
>> >> > Tim Bhatnagar
>> >> > PhD Candidate
>> >> > Orthopaedic Injury Biomechanics Group
>> >> > Department of Mechanical Engineering
>> >> > University of British Columbia
>> >> >
>> >> > Rm 5000 - 818 West 10th Ave.
>> >> > Vancouver, BC
>> >> > Canada
>> >> > V5Z 1M9
>> >> >
>> >> > Ph: (604) 675-8845
>> >> > Fax: (604) 675-8820
>> >> > Web: oibg.mech.ubc.ca
>> >> >
>> >> > _____________________________________
>> >> > Powered by www.kitware.com
>> >> >
>> >> > Visit other Kitware open-source projects at
>> >> > http://www.kitware.com/opensource/opensource.html
>> >> >
>> >> > Kitware offers ITK Training Courses, for more information visit:
>> >> > http://www.kitware.com/products/protraining.php
>> >> >
>> >> > Please keep messages on-topic and check the ITK FAQ at:
>> >> > http://www.itk.org/Wiki/ITK_FAQ
>> >> >
>> >> > Follow this link to subscribe/unsubscribe:
>> >> > http://www.itk.org/mailman/listinfo/insight-users
>> >> >
>> >
>> >
>> >
>> >
>> > --
>> > Tim Bhatnagar
>> > PhD Candidate
>> > Orthopaedic Injury Biomechanics Group
>> > Department of Mechanical Engineering
>> > University of British Columbia
>> >
>> > Rm 5000 - 818 West 10th Ave.
>> > Vancouver, BC
>> > Canada
>> > V5Z 1M9
>> >
>> > Ph: (604) 675-8845
>> > Fax: (604) 675-8820
>> > Web: oibg.mech.ubc.ca
>>
>
>
>
> --
> Tim Bhatnagar
> PhD Candidate
> Orthopaedic Injury Biomechanics Group
> Department of Mechanical Engineering
> University of British Columbia
>
> Rm 5000 - 818 West 10th Ave.
> Vancouver, BC
> Canada
> V5Z 1M9
>
> Ph: (604) 675-8845
> Fax: (604) 675-8820
> Web: oibg.mech.ubc.ca
>



-- 
Tim Bhatnagar
PhD Candidate
Orthopaedic Injury Biomechanics Group
Department of Mechanical Engineering
University of British Columbia

Rm 5000 - 818 West 10th Ave.
Vancouver, BC
Canada
V5Z 1M9

Ph: (604) 675-8845
Fax: (604) 675-8820
Web: oibg.mech.ubc.ca
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://www.itk.org/pipermail/insight-users/attachments/20131012/3e63114f/attachment.htm>