<div dir="ltr"><div>Hmmm,<br><br></div>The coordinate system from my raw data matches up with my vtk data (not disp fields, the actual image data) imported into Paraview for visualization, as well as used in ITK to generate displacement fields. If the coordinate systems of my input images are the same, is there any reason why my displacement field should be in different coordinates?<br>
</div><div class="gmail_extra"><br><br><div class="gmail_quote">On Wed, Oct 9, 2013 at 11:06 AM, Matt McCormick <span dir="ltr"><<a href="mailto:matt.mccormick@kitware.com" target="_blank">matt.mccormick@kitware.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Hi Tim,<br>
<br>
If viewing the data with VTK or other library, deformation in the<br>
negative y-direction should be taken with care because of a difference<br>
in coordinate systems [1].<br>
<br>
HTH,<br>
Matt<br>
<br>
[1] <a href="http://www.slicer.org/slicerWiki/index.php/Slicer:VTK_ITK_Coordinates" target="_blank">http://www.slicer.org/slicerWiki/index.php/Slicer:VTK_ITK_Coordinates</a><br>
<div class="HOEnZb"><div class="h5"><br>
On Wed, Oct 9, 2013 at 5:59 PM, Tim Bhatnagar <<a href="mailto:tim.bhatnagar@gmail.com">tim.bhatnagar@gmail.com</a>> wrote:<br>
> Thanks Matt,<br>
><br>
> It is strange then, that I can extract data from the displacement field that<br>
> seems to represent the field that would transform the 'pre-deformation'<br>
> image into the 'deformation' image. (There is a significant deformation in<br>
> the 'deformation data' in the negative y-direction, which shows up nicely in<br>
> the displacement field.<br>
><br>
> Must I be doing something strange for this to happen?<br>
><br>
><br>
> On Wed, Oct 9, 2013 at 10:31 AM, Matt McCormick <<a href="mailto:matt.mccormick@kitware.com">matt.mccormick@kitware.com</a>><br>
> wrote:<br>
>><br>
>> Hi Tim,<br>
>><br>
>> No, the WarpImageFilter should be generating a 'pre-deformation'<br>
>> look-alike. For more information, see the Software Guide.<br>
>><br>
>> HTH,<br>
>> Matt<br>
>><br>
>> On Wed, Oct 9, 2013 at 4:48 PM, Tim Bhatnagar <<a href="mailto:tim.bhatnagar@gmail.com">tim.bhatnagar@gmail.com</a>><br>
>> wrote:<br>
>> > Hello all,<br>
>> ><br>
>> > I use the ITK examples ImageRegistration5, ImageRegistration8 and<br>
>> > DeformableRegistration2 (Demon's) for registration of normal and<br>
>> > deformed<br>
>> > data (same subject). Briefly, I do some pre-registration of my data<br>
>> > using<br>
>> > ImageReg5 and ImageReg8 (for gross alignment), after which I take the<br>
>> > produced displacement fields, and use them as the 'initial displacement<br>
>> > field' for DefReg2.<br>
>> ><br>
>> > In all cases, I am using my 'pre-deformation' data as my fixed source,<br>
>> > and<br>
>> > my 'deformation' data as my moving source.<br>
>> ><br>
>> > I have some fiducial markers to check the accuracy of the generated<br>
>> > displacement field, and it looks pretty good. However, when trying to<br>
>> > produce figures, my registration output looks much closer to my<br>
>> > 'deformation' data, and sometimes the output and the actual<br>
>> > 'deformation'<br>
>> > data are offset by a magnitude.<br>
>> ><br>
>> > In my situation, should I be aiming to have my registration output<br>
>> > appear<br>
>> > similar to my 'pre-deformation' data? (I get confused reading the ITK<br>
>> > explanation on that) Shouldn't I be able to produce the a 'deformation'<br>
>> > look-a-like by using WarpImageFilter with my 'pre-deformation' data and<br>
>> > my<br>
>> > generated displacement field?<br>
>> ><br>
>> > Sorry this was so wordy. Any help would be much appreciated.<br>
>> ><br>
>> > --<br>
>> > Tim Bhatnagar<br>
>> > PhD Candidate<br>
>> > Orthopaedic Injury Biomechanics Group<br>
>> > Department of Mechanical Engineering<br>
>> > University of British Columbia<br>
>> ><br>
>> > Rm 5000 - 818 West 10th Ave.<br>
>> > Vancouver, BC<br>
>> > Canada<br>
>> > V5Z 1M9<br>
>> ><br>
>> > Ph: (604) 675-8845<br>
>> > Fax: (604) 675-8820<br>
>> > Web: <a href="http://oibg.mech.ubc.ca" target="_blank">oibg.mech.ubc.ca</a><br>
>> ><br>
>> > _____________________________________<br>
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><br>
><br>
><br>
><br>
> --<br>
> Tim Bhatnagar<br>
> PhD Candidate<br>
> Orthopaedic Injury Biomechanics Group<br>
> Department of Mechanical Engineering<br>
> University of British Columbia<br>
><br>
> Rm 5000 - 818 West 10th Ave.<br>
> Vancouver, BC<br>
> Canada<br>
> V5Z 1M9<br>
><br>
> Ph: <a href="tel:%28604%29%20675-8845" value="+16046758845">(604) 675-8845</a><br>
> Fax: <a href="tel:%28604%29%20675-8820" value="+16046758820">(604) 675-8820</a><br>
> Web: <a href="http://oibg.mech.ubc.ca" target="_blank">oibg.mech.ubc.ca</a><br>
</div></div></blockquote></div><br><br clear="all"><br>-- <br>Tim Bhatnagar<br>PhD Candidate<br>Orthopaedic Injury Biomechanics Group<br>Department of Mechanical Engineering<br>University of British Columbia<br><br>Rm 5000 - 818 West 10th Ave.<br>
Vancouver, BC<br>Canada<br>V5Z 1M9<br><br>Ph: (604) 675-8845<br>Fax: (604) 675-8820<br>Web: <a href="http://oibg.mech.ubc.ca" target="_blank">oibg.mech.ubc.ca</a><br>
</div>