<div dir="ltr"><div>Hello again,<br><br></div>I've found this snippet of code on ITK/VTK forums:<br><br><pre><code>FlipFilterType::Pointer flipperImage = FlipFilterType::New();
bool flipAxes[3] = { false, true, false };
flipperImage = FlipFilterType::New();
flipperImage->SetFlipAxes(flipAxes);
flipperImage->SetInput( image );
flipperImage->Update();<br><br></code></pre><pre><code><span style="font-family:arial,helvetica,sans-serif">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?<br>
<br>Thanks again,<br></span></code></pre><br></div><div class="gmail_extra"><br><br><div class="gmail_quote">On Sat, Oct 12, 2013 at 12:31 PM, Tim Bhatnagar <span dir="ltr"><<a href="mailto:tim.bhatnagar@gmail.com" target="_blank">tim.bhatnagar@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr"><div><div><div>Hello all,<br><br></div>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?<br>
<br></div>I was pointed to this source: <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> , 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).<br>
<br></div>A bit of an explanation would really help. Thank you!<br><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><div><br>
On Wed, Oct 9, 2013 at 5:59 PM, Tim Bhatnagar <<a href="mailto:tim.bhatnagar@gmail.com" target="_blank">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" target="_blank">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" target="_blank">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: <a href="tel:%28604%29%20675-8845" value="+16046758845" target="_blank">(604) 675-8845</a><br>
>> > Fax: <a href="tel:%28604%29%20675-8820" value="+16046758820" target="_blank">(604) 675-8820</a><br>
>> > Web: <a href="http://oibg.mech.ubc.ca" target="_blank">oibg.mech.ubc.ca</a><br>
>> ><br>
>> > _____________________________________<br>
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>> ><br>
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>> ><br>
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>> ><br>
><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" target="_blank">(604) 675-8845</a><br>
> Fax: <a href="tel:%28604%29%20675-8820" value="+16046758820" target="_blank">(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: <a href="tel:%28604%29%20675-8845" value="+16046758845" target="_blank">(604) 675-8845</a><br>Fax: <a href="tel:%28604%29%20675-8820" value="+16046758820" target="_blank">(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>