<html><body><div style="color:#000; background-color:#fff; font-family:times new roman, new york, times, serif;font-size:12pt"><div class="" style="">Hi Nicolas, Matt,</div><div class="" style=""><br class="" style=""></div><div style="color: rgb(0, 0, 0); font-size: 16px; font-family: 'times new roman', 'new york', times, serif; font-style: normal; background-color: transparent;" class="">Finally I found out what the problem was.</div><div style="color: rgb(0, 0, 0); font-size: 16px; font-family: 'times new roman', 'new york', times, serif; font-style: normal; background-color: transparent;" class="">I had to : SetInput (roi_filter->GetOutput() ) to the Fast marching filter , other than specifying : fastMarching->SetOutputSize( rescaleFilter->GetOutput()->GetBufferedRegion().GetSize() );</div><div style="color: rgb(0, 0, 0); font-size: 16px; font-family: 'times new roman', 'new york', times, serif; font-style: normal;
background-color: transparent;" class=""><br class="" style=""></div><div style="color: rgb(0, 0, 0); font-size: 16px; font-family: 'times new roman', 'new york', times, serif; font-style: normal; background-color: transparent;" class="">below link helped me :</div><div style="background-color: transparent;" class="">http://www.itk.org/pipermail/insight-users/2010-May/036993.html<br class="" style=""></div><div style="color: rgb(0, 0, 0); font-size: 16px; font-family: 'times new roman', 'new york', times, serif; font-style: normal; background-color: transparent;" class=""><br class="" style=""></div><div style="background-color: transparent;" class="">I think in ITK manual : this is given in words like :<span style="font-weight: bold;"> <span style="background-color: transparent;" class="">Note that the size is obtained here from</span></span></div><div style="background-color: transparent;" class=""><span style="font-weight: bold;">the output
image of the smoothing filter. The size of this image is valid only after the Update()</span></div><div style="background-color: transparent;" class=""><span style="font-weight: bold;">methods of this filter have been called directly or indirectly........ page 503</span></div><div style="color: rgb(0, 0, 0); font-size: 16px; font-family: 'times new roman', 'new york', times, serif; font-style: normal; background-color: transparent;" class=""><span style="font-weight: bold;"><br></span></div><div style="color: rgb(0, 0, 0); font-size: 16px; font-family: 'times new roman', 'new york', times, serif; font-style: normal; background-color: transparent;" class="">anyway thanks for your help :)</div><div style="color: rgb(0, 0, 0); font-size: 16px; font-family: 'times new roman', 'new york', times, serif; font-style: normal; background-color: transparent;" class=""><br class="" style=""></div> <div class="qtdSeparateBR"><br><br></div><div class="yahoo_quoted"
style="display: block;"> <div style="font-family: times new roman, new york, times, serif; font-size: 12pt;" class=""> <div style="font-family: times new roman, new york, times, serif; font-size: 12pt;" class=""> <div dir="ltr" class="" style=""> <font size="2" face="Arial" class="" style=""> On Wednesday, 18 June 2014 11:29 AM, Sindhoor Bhat <bhatsindhoor@ymail.com> wrote:<br class="" style=""> </font> </div> <br class="" style=""><br class="" style=""> <div class="" style=""><div id="yiv5566337092" class="" style=""><div class="" style=""><div style="color:#000;background-color:#fff;font-family:times new roman, new york, times, serif;font-size:12pt;" class=""><div class="" style="">Hi Matt,</div><div class="" style="">Here is the error. </div><div class="" style="">vtkImageImport (0000000002750400): Calling UpdateInformationCallback: c:\itk file\source\modules\core\common\include\itkImageToImageFilter.hxx:248:<br clear="none" class=""
style=""></div><div class="" style="color:rgb(0, 0, 0);font-size:16px;font-family:'times new roman', 'new york', times, serif;font-style:normal;background-color:transparent;"><br clear="none" class="" style=""></div><div class="" style="color:rgb(0, 0, 0);font-size:16px;font-family:'times new roman', 'new york', times, serif;font-style:normal;background-color:transparent;">When I checked a lot on itk forums, it was mentioned that this problem is due to some ITK version update .</div><div class="" style="color:rgb(0, 0, 0);font-size:16px;font-family:'times new roman', 'new york', times, serif;font-style:normal;background-color:transparent;">Really dont know what the problem is,</div><div class="" style="color:rgb(0, 0, 0);font-size:16px;font-family:'times new roman', 'new york', times, serif;font-style:normal;background-color:transparent;">I removed ROI filter etc but still problem exists</div><div class="" style="color:rgb(0, 0,
0);font-size:16px;font-family:'times new roman', 'new york', times, serif;font-style:normal;background-color:transparent;">can you pls tell what the problem is.</div> <div class="" style=""><br clear="none" class="" style=""><br clear="none" class="" style=""></div><div class="" id="yiv5566337092yqt70774" style=""><div class="" style="display:block;"> <div class="" style="font-family:times new roman, new york, times, serif;font-size:12pt;"> <div class="" style="font-family:times new roman, new york, times, serif;font-size:12pt;"> <div class="" dir="ltr" style=""> <font class="" size="2" face="Arial" style=""> On Tuesday, 17 June 2014 7:38 PM, Matt McCormick
<matt.mccormick@kitware.com> wrote:<br clear="none" class="" style=""> </font> </div> <br clear="none" class="" style=""><br clear="none" class="" style=""> <div class="" style="">Hi Sindhoor,<br clear="none" class="" style=""><br clear="none" class="" style="">Look at image->GetLargestPossibleRegion() to reveal if that is a valid<br clear="none" class="" style="">index inside the image.<br clear="none" class="" style=""><br clear="none" class="" style="">Make sure the Image Origin and Spacing are as expected.<br clear="none" class="" style=""><br clear="none" class="" style="">The ITK Software Guide [1] has a good explanation on the relationship<br clear="none" class="" style="">between index space and physical space.<br clear="none" class="" style=""><br clear="none" class="" style="">Hope this helps,<br clear="none" class="" style="">Matt<br clear="none" class="" style=""><br clear="none" class="" style="">[1] <a rel="nofollow" shape="rect"
class="" target="_blank" href="http://itk.org/ItkSoftwareGuide.pdf" style="">http://itk.org/ItkSoftwareGuide.pdf</a><br clear="none" class="" style=""><div class="" id="yiv5566337092yqtfd19883" style=""><br clear="none" class="" style="">On Mon, Jun 9, 2014 at 11:51 AM, Sindhoor Bhat <<a rel="nofollow" shape="rect" class="" ymailto="mailto:bhatsindhoor@ymail.com" target="_blank" href="mailto:bhatsindhoor@ymail.com" style="">bhatsindhoor@ymail.com</a>> wrote:<br clear="none" class="" style="">> Hi Matt /ITK<br clear="none" class="" style="">><br clear="none" class="" style="">> Using TransformPhysicalPointToIndex I was able to get pixel index.<br clear="none" class="" style="">> But in Z direction I've got negative value 44, 61, -157<br clear="none" class="" style="">><br clear="none" class="" style="">> I want to use this point as seed. But When I use this am getting black<br clear="none" class="" style="">> screen as
output.<br clear="none" class="" style="">><br clear="none" class="" style="">> Is it ok
to use -ve Z or should I do changes?<br clear="none" class="" style="">><br clear="none" class="" style="">> Also image index is not at the bottom left corner as mentioned in ITK<br clear="none" class="" style="">> manual. it is somewhere near mid bottom end<br clear="none" class="" style="">><br clear="none" class="" style="">> Can you pls give some light on this?<br clear="none" class="" style="">> thanks<br clear="none" class="" style="">><br clear="none" class="" style="">><br clear="none" class="" style="">><br clear="none" class="" style="">><br clear="none" class="" style="">><br clear="none" class="" style="">><br clear="none" class="" style="">><br clear="none" class="" style="">> On Sunday, 8 June 2014 8:34 AM, Sindhoor Bhat <<a rel="nofollow" shape="rect" class="" ymailto="mailto:bhatsindhoor@ymail.com" target="_blank" href="mailto:bhatsindhoor@ymail.com" style="">bhatsindhoor@ymail.com</a>><br
clear="none" class="" style="">> wrote:<br clear="none" class="" style="">><br clear="none" class="" style="">><br clear="none" class="" style="">> thanks Matt. Will try this.<br clear="none" class="" style="">><br clear="none" class="" style="">><br clear="none" class="" style="">> On Sunday, 8 June 2014 1:09 AM, Matt McCormick <<a rel="nofollow" shape="rect" class="" ymailto="mailto:matt.mccormick@kitware.com" target="_blank" href="mailto:matt.mccormick@kitware.com" style="">matt.mccormick@kitware.com</a>><br clear="none" class="" style="">> wrote:<br clear="none" class="" style="">><br clear="none" class="" style="">><br clear="none" class="" style="">> Hi Sindoor,<br clear="none" class="" style="">><br clear="none" class="" style="">> itk::Image contains methods like TransformPhysicalPointToIndex [1]<br clear="none" class="" style="">> that can be helpful.<br clear="none" class="" style="">><br
clear="none" class="" style="">> Matt<br clear="none" class="" style="">><br clear="none" class="" style="">> [1]<br clear="none" class="" style="">> <a rel="nofollow" shape="rect" class="" target="_blank" href="http://www.itk.org/Doxygen/html/classitk_1_1ImageBase.html#af4a7c9c3787e9fdafbaaade2e02efa25" style="">http://www.itk.org/Doxygen/html/classitk_1_1ImageBase.html#af4a7c9c3787e9fdafbaaade2e02efa25</a><br clear="none" class="" style="">><br clear="none" class="" style="">> On Sat, Jun 7, 2014 at 7:09 AM, Sindhoor Bhat <<a rel="nofollow" shape="rect" class="" ymailto="mailto:bhatsindhoor@ymail.com" target="_blank" href="mailto:bhatsindhoor@ymail.com" style="">bhatsindhoor@ymail.com</a>><br clear="none" class="" style="">> wrote:<br clear="none" class="" style="">>> Dear Matt/itk users,<br clear="none" class="" style="">>> Now I'm able to pick world coordinates using vtk point picker widget.<br clear="none"
class="" style="">>> But for seed input to itk, we need index. I'm really struck. can you
pls<br clear="none" class="" style="">>> help me how to move further? using itk-vtk interaction for seed selection?<br clear="none" class="" style="">>><br clear="none" class="" style="">>> Also, to call vtk window for point selection which command should i use?<br clear="none" class="" style="">>> (is<br clear="none" class="" style="">>> it call-back function in vtk? But from itk how to call ?)<br clear="none" class="" style="">>><br clear="none" class="" style="">>> thank you<br clear="none" class="" style="">>><br clear="none" class="" style="">>><br clear="none" class="" style="">>> On Friday, 6 June 2014 6:04 PM, Matt McCormick<br clear="none" class="" style="">>> <<a rel="nofollow" shape="rect" class="" ymailto="mailto:matt.mccormick@kitware.com" target="_blank" href="mailto:matt.mccormick@kitware.com" style="">matt.mccormick@kitware.com</a>><br clear="none" class=""
style="">>> wrote:<br clear="none" class="" style="">>><br clear="none" class="" style="">>><br clear="none" class="" style="">>> Hi Sindhoor,<br clear="none" class="" style="">>><br clear="none" class="" style="">>> In your previous mail, you described taking sub-regions, which changes<br clear="none" class="" style="">>> index positions. To sample a value from a physical position, use an<br clear="none" class="" style="">>> itk::InterpolateImageFunction.<br clear="none" class="" style="">>><br clear="none" class="" style="">>> The apparent flip may be due to a difference in the direction and<br clear="none" class="" style="">>> location of the Y-axis in your visualization programs.<br clear="none" class="" style="">>><br clear="none" class="" style="">>> Hope this helps,<br clear="none" class="" style="">>> Matt<br clear="none" class="" style="">>><br
clear="none" class="" style="">>> On
Fri, Jun 6, 2014 at 1:03 AM, Sindhoor Bhat <<a rel="nofollow" shape="rect" class="" ymailto="mailto:bhatsindhoor@ymail.com" target="_blank" href="mailto:bhatsindhoor@ymail.com" style="">bhatsindhoor@ymail.com</a>><br clear="none" class="" style="">>> wrote:<br clear="none" class="" style="">>>> Thanks Matt for your suggestion.<br clear="none" class="" style="">>>> *But I've tried with that too. It is not considering the index/seed<br clear="none" class="" style="">>>> position<br clear="none" class="" style="">>>> that I write in program.<br clear="none" class="" style="">>>> When I added below code to get selected seed position, it shows<br clear="none" class="" style="">>>> completely different point than what I had written(using image J ---><br clear="none" class="" style="">>>> physical coordinates )<br clear="none" class="" style="">>>>
std::cout << filter->GetOutput()->GetPixel( Position1 )<br clear="none" class="" style="">>>> <<<br clear="none" class="" style="">>>> std::endl;<br clear="none" class="" style="">>>> *seed point doesn't appear between selected thresholds ( say: (85,300) &<br clear="none" class="" style="">>>> seep position will be like 45 etc)<br clear="none" class="" style="">>>><br clear="none" class="" style="">>>> *Also, I should mention that my dicom images appear in reverse order(<br clear="none" class="" style="">>>> flipped). Is this affecting my seed selection?<br clear="none" class="" style="">>>> (I tried subtracting Y coordinate from maxY etc.)<br clear="none" class="" style="">>>><br clear="none" class="" style="">>>> Can you pls tell what is wrong? thank you.<br clear="none" class=""
style="">>>><br clear="none" class="" style="">>><br clear="none" class="" style="">>><br clear="none" class="" style="">><br clear="none" class="" style="">><br clear="none" class="" style="">><br clear="none" class="" style="">><br clear="none" class="" style=""></div><br clear="none" class="" style=""><br clear="none" class="" style=""></div> </div> </div> </div></div> </div></div></div><br class="" style=""><br class="" style=""></div> </div> </div> </div> </div></body></html>