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

[Tim Bhatnagar]

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
> >> >
> >> > _____________________________________
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> >
> >
> >
> >
> > --
> > 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
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