<p dir="ltr">Hello Andrew,</p>
<p dir="ltr">Another thing you can look at is if your transform parameters ratios are set to reasonable values. You typically have a ratio you can set between rotation, translation, scaling. If these are not set to appropriate values, the final transform could be wrong.<br>
In your case, it sounds like you are already performing the translation as an initialization. Maybe you can modify your parameters so that it performs mostly a rotation.</p>
<p dir="ltr">Hope this helps,<br>
François</p>
<br><div class="gmail_quote"><div dir="ltr">On Tue, Apr 11, 2017, 14:07 Dženan Zukić <<a href="mailto:dzenanz@gmail.com">dzenanz@gmail.com</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr" class="gmail_msg"><div class="gmail_default gmail_msg" style="font-family:verdana,sans-serif;font-size:small">Hi Andrew,</div><div class="gmail_default gmail_msg" style="font-family:verdana,sans-serif;font-size:small"><br class="gmail_msg"></div><div class="gmail_default gmail_msg" style="font-family:verdana,sans-serif;font-size:small">it is good to use such additional constraints when possible. But you also have to initialize the transform somehow, otherwise it might get auto-initialized to all modifiable parameters being equal to zero. That is usually a bad initial transform - hence Francois' suggestion.</div><div class="gmail_default gmail_msg" style="font-family:verdana,sans-serif;font-size:small"><div dir="ltr" class="gmail_msg"><div class="gmail_default gmail_msg" style="font-family:verdana,sans-serif;font-size:small"><br class="gmail_msg"></div><div class="gmail_default gmail_msg" style="font-family:verdana,sans-serif;font-size:small">Regards,</div><div class="gmail_default gmail_msg"><font face="verdana, sans-serif" class="gmail_msg">Dženan Zukić, PhD, Senior R&D Engineer, Kitware (Carrboro, N.C.)</font></div></div></div></div><div class="gmail_extra gmail_msg"><br class="gmail_msg"><div class="gmail_quote gmail_msg">On Tue, Apr 11, 2017 at 2:02 PM, Andrew Harris <span dir="ltr" class="gmail_msg"><<a href="mailto:aharr8@uwo.ca" class="gmail_msg" target="_blank">aharr8@uwo.ca</a>></span> wrote:<br class="gmail_msg"><blockquote class="gmail_quote gmail_msg" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr" class="gmail_msg">Hello Francois and Dženan,<div class="gmail_msg"><br class="gmail_msg"></div><div class="gmail_msg">Because of the way the images were captured, there is a known common point of overlap, so we set the centre to that point in the expectation that the transform would rotate and translate about that point when the registration is run.  Have I misunderstood the design or is that what should be happening?</div></div><div class="gmail_extra gmail_msg"><span class="gmail_msg"><br clear="all" class="gmail_msg"><div class="gmail_msg"><div class="m_-6604079760106629441m_-4600384429698437568gmail_signature gmail_msg" data-smartmail="gmail_signature"><div dir="ltr" class="gmail_msg"><div class="gmail_msg"><div dir="ltr" class="gmail_msg"><div class="gmail_msg"><div dir="ltr" class="gmail_msg"><div class="gmail_msg"><div dir="ltr" class="gmail_msg"><p class="gmail_msg">--</p><p class="gmail_msg">AH<br class="gmail_msg"></p><p class="gmail_msg"><br class="gmail_msg"></p><p class="gmail_msg">-----------------------------------------------------------------------------------------------</p><p class="gmail_msg"><i class="gmail_msg">This email and any attachments thereto may contain private, confidential, and privileged materials for the sole use of the intended recipient. Any reviewing, copying, or distribution of this email (or any attachments thereto) by other than the intended recipient is strictly prohibited. If you are not the intended recipient, please contact the sender immediately and permanently destroy this email and any attachments thereto.</i></p></div></div></div></div></div></div></div></div></div>
<br class="gmail_msg"></span><div class="gmail_msg"><div class="m_-6604079760106629441h5 gmail_msg"><div class="gmail_quote gmail_msg">On Tue, Apr 11, 2017 at 9:00 AM, Francois Budin <span dir="ltr" class="gmail_msg"><<a href="mailto:francois.budin@kitware.com" class="gmail_msg" target="_blank">francois.budin@kitware.com</a>></span> wrote:<br class="gmail_msg"><blockquote class="gmail_quote gmail_msg" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr" class="gmail_msg"><div class="gmail_msg"><div class="gmail_msg"><div class="gmail_msg"><div class="gmail_msg">Hello Andrew,<br class="gmail_msg"><br class="gmail_msg"></div>Did you try to initialize the registration with [1] for example?<br class="gmail_msg"></div>If the images do not overlap at all at the beginning of the registration, the algorithm might only do what Dżenan said, match black pixels.<br class="gmail_msg"></div>Initializing the transform should help.<br class="gmail_msg"><br class="gmail_msg"></div><div class="gmail_msg">Hope this helps,<br class="gmail_msg"></div>Francois<br class="gmail_msg"><div class="gmail_msg"><div class="gmail_msg"><div class="gmail_msg"><br class="gmail_msg">[1] <a href="https://itk.org/Doxygen/html/classitk_1_1CenteredTransformInitializer.html" class="gmail_msg" target="_blank">https://itk.org/Doxygen/html/classitk_1_1CenteredTransformInitializer.html</a><br class="gmail_msg"></div></div></div></div><div class="m_-6604079760106629441m_-4600384429698437568HOEnZb gmail_msg"><div class="m_-6604079760106629441m_-4600384429698437568h5 gmail_msg"><div class="gmail_extra gmail_msg"><br class="gmail_msg"><div class="gmail_quote gmail_msg">On Tue, Apr 11, 2017 at 8:36 AM, Andrew Harris <span dir="ltr" class="gmail_msg"><<a href="mailto:aharr8@uwo.ca" class="gmail_msg" target="_blank">aharr8@uwo.ca</a>></span> wrote:<br class="gmail_msg"><blockquote class="gmail_quote gmail_msg" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr" class="gmail_msg">In the image mask, the parts we want to include in the calculation are bright and the parts that we want to exclude are dark, is that the opposite of what it should be?</div><div class="gmail_extra gmail_msg"><span class="gmail_msg"><br clear="all" class="gmail_msg"><div class="gmail_msg"><div class="m_-6604079760106629441m_-4600384429698437568m_7855588344141137896m_2892137538414551205gmail_signature gmail_msg" data-smartmail="gmail_signature"><div dir="ltr" class="gmail_msg"><div class="gmail_msg"><div dir="ltr" class="gmail_msg"><div class="gmail_msg"><div dir="ltr" class="gmail_msg"><div class="gmail_msg"><div dir="ltr" class="gmail_msg"><p class="gmail_msg">--</p><p class="gmail_msg">AH<br class="gmail_msg"></p><p class="gmail_msg"><br class="gmail_msg"></p><p class="gmail_msg">-----------------------------------------------------------------------------------------------</p><p class="gmail_msg"><i class="gmail_msg">This email and any attachments thereto may contain private, confidential, and privileged materials for the sole use of the intended recipient. Any reviewing, copying, or distribution of this email (or any attachments thereto) by other than the intended recipient is strictly prohibited. If you are not the intended recipient, please contact the sender immediately and permanently destroy this email and any attachments thereto.</i></p></div></div></div></div></div></div></div></div></div>
<br class="gmail_msg"></span><div class="gmail_msg"><div class="m_-6604079760106629441m_-4600384429698437568m_7855588344141137896h5 gmail_msg"><div class="gmail_quote gmail_msg">On Thu, Mar 30, 2017 at 7:25 PM, Dženan Zukić <span dir="ltr" class="gmail_msg"><<a href="mailto:dzenanz@gmail.com" class="gmail_msg" target="_blank">dzenanz@gmail.com</a>></span> wrote:<br class="gmail_msg"><blockquote class="gmail_quote gmail_msg" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr" class="gmail_msg"><div class="gmail_default gmail_msg" style="font-family:verdana,sans-serif;font-size:small">Hi Andrew,</div><div class="gmail_default gmail_msg" style="font-family:verdana,sans-serif;font-size:small"><br class="gmail_msg"></div><div class="gmail_default gmail_msg" style="font-family:verdana,sans-serif;font-size:small">your masks might be inverted. If NCC gets all black pixels in both images, the correlation will be perfect.</div><div class="gmail_default gmail_msg" style="font-family:verdana,sans-serif;font-size:small"><br class="gmail_msg"></div><div class="gmail_default gmail_msg" style="font-family:verdana,sans-serif;font-size:small">Regards,</div><div class="gmail_default gmail_msg" style="font-family:verdana,sans-serif;font-size:small">Dženan</div></div><div class="gmail_extra gmail_msg"><br class="gmail_msg"><div class="gmail_quote gmail_msg"><div class="gmail_msg"><div class="m_-6604079760106629441m_-4600384429698437568m_7855588344141137896m_2892137538414551205h5 gmail_msg">On Thu, Mar 30, 2017 at 2:13 PM, Andrew Harris <span dir="ltr" class="gmail_msg"><<a href="mailto:aharr8@uwo.ca" class="gmail_msg" target="_blank">aharr8@uwo.ca</a>></span> wrote:<br class="gmail_msg"></div></div><blockquote class="gmail_quote gmail_msg" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div class="gmail_msg"><div class="m_-6604079760106629441m_-4600384429698437568m_7855588344141137896m_2892137538414551205h5 gmail_msg"><div dir="ltr" class="gmail_msg">Hi, I'm hoping someone can guide me toward an explanation of this.  I run my pipeline on various ultrasound image sets and get an NCC between 0.65 and 0.8 for good alignments, but on some sets the NCC returns 1.0 when the images aren't even overlapping.  I have the black areas of the image masked out, and have even tried cranking up the threshold to be sure the darker areas aren't being included to no avail.  Any thoughts?<br clear="all" class="gmail_msg"><div class="gmail_msg"><div class="m_-6604079760106629441m_-4600384429698437568m_7855588344141137896m_2892137538414551205m_-5255256472375010337m_8305282680372223308gmail_signature gmail_msg" data-smartmail="gmail_signature"><div dir="ltr" class="gmail_msg"><div class="gmail_msg"><div dir="ltr" class="gmail_msg"><div class="gmail_msg"><div dir="ltr" class="gmail_msg"><div class="gmail_msg"><div dir="ltr" class="gmail_msg"><p class="gmail_msg">--</p><p class="gmail_msg">AH<br class="gmail_msg"></p><p class="gmail_msg"><br class="gmail_msg"></p><p class="gmail_msg">-----------------------------------------------------------------------------------------------</p><p class="gmail_msg"><i class="gmail_msg">This email and any attachments thereto may contain private, confidential, and privileged materials for the sole use of the intended recipient. Any reviewing, copying, or distribution of this email (or any attachments thereto) by other than the intended recipient is strictly prohibited. If you are not the intended recipient, please contact the sender immediately and permanently destroy this email and any attachments thereto.</i></p></div></div></div></div></div></div></div></div></div>
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