<html><body><div style="color:#000; background-color:#fff; font-family:times new roman, new york, times, serif;font-size:12pt"><div class="" style=""><span class="" style="">Hi Nicolas,</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 class="" style=""><br class="" style=""></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 class="" style="">Thanks for reply. This is what I did . Added below code to all filters & got origin & spacing of image</span></div><div style="background-color: transparent;" class=""><br class="" style=""></div><div style="background-color: transparent;" class=""><span class="" style="white-space:pre"> </span>
OutputImageType:: Pointer image2= sigmoidFilter->GetOutput();</div><div style="background-color: transparent;" class=""><span class="" style=""></span></div><div style="background-color: transparent;" class=""> image2->Print( std::cout ). </div><div style="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="">But there is no problem with all the filters used. <span style="background-color: transparent;">There is a problem when it comes to fast marching. </span></div><div style="background-color: transparent;" class=""> fastMarching->SetOutputSize(
roi_filter->GetOutput()->GetBufferedRegion().GetSize() ); <span style="color: rgb(68, 0, 98);">//took o/p from roi filter (after reading---ROI----gradient magnitude etc )</span><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></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="">* In itk manual I've one doubt (image attached). <span style="font-weight: bold;">They say take buffer region from smoothing filter , but have taken o/p from reader. That is not clear. </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=""><span>Can you pls tell what is wrong?</span></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 Tuesday, 17 June 2014 2:26 PM, Nicolas Gallego <nicgallego@gmail.com> wrote:<br class="" style=""> </font> </div> <br class="" style=""><br class="" style=""> <div class="" style=""><div id="yiv9794055451" class="" style=""><div class="" style=""><div dir="ltr" class="" style=""><div class="" style=""><div class="" style=""><div class=""
style=""><div class="" style=""><div class="" style=""><div class="" style=""><div class="" style=""><div class="" style="">Hi Sindhoor,<br clear="none" class="" style=""><br clear="none" class="" style=""></div>It's hard to tell. Could you provide a simple code that reproduces your error?<br clear="none" class="" style=""></div>A priori I would say you could print the image information on each connection of your pipeline, pay special attention to filters that may change it, as the ROI filter...<br clear="none" class="" style="">
</div>Refer also to the concepts of regions: there are<br clear="none" class="" style=""></div>LargestPossibleRegion<br clear="none" class="" style=""></div>BufferedRegion<br clear="none" class="" style=""></div>RequestedRegion<br clear="none" class="" style=""><br clear="none" class="" style=""></div>LargestPossibleRegion refers to the whole dataset. Refer to section 13.1 of the software guide for more details.<br clear="none" class="" style="">
</div>I hope that helps,<br clear="none" class="" style=""><div class="" style=""><br clear="all" class="" style=""><div class="" style=""><div dir="ltr" class="" style="">Nicolás Gallego-Ortiz<br clear="none" class="" style="">Université catholique de Louvain, Belgium<br clear="none" class="" style=""></div></div>
<br clear="none" class="" style=""><br clear="none" class="" style=""><div class="" style="">2014-06-17 10:36 GMT+02:00 Sindhoor Bhat <span dir="ltr" class="" style=""><<a rel="nofollow" shape="rect" ymailto="mailto:bhatsindhoor@ymail.com" target="_blank" href="mailto:bhatsindhoor@ymail.com" class="" style="">bhatsindhoor@ymail.com</a>></span>:<br clear="none" class="" style=""><div class="" id="yiv9794055451yqt15586" style=""><blockquote class="" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
<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=""><span class="" style="">Hi nicgallego,</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 class="" style="">Thanks for reply.</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 class="" style="">I've read that section. Here is some detail on steps i followed. This may help you to give some hints.</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 class="" style=""><br clear="none" class="" style=""></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 class="" style="">1.read dicom series</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 class="" style="">2.define region of interest (ROI filter)</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="">3. compute gradient & speed image.</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="">
4.Set seed using fast marching filter.</div><div class="" style="">5.Give this inital level set image---- to geodesic segmentation filter</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 class="" style=""><br clear="none" class="" style=""></span></div><div style="background-color:transparent;" class=""> geodesicActiveContour->SetInput( fastMarching->GetOutput() );</div><div style="background-color:transparent;" class=""> geodesicActiveContour->SetFeatureImage( sigmoidFilter->GetOutput() );</div>
<div style="background-color:transparent;" class=""><br clear="none" 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="">
fastMarching->SetOutputSize(roi_filter->GetOutput()->GetBufferedRegion().GetSize() ); //roi=region of interest<br clear="none" 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 clear="none" 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=""> Even after reading from same dicom series, why is this error? it should have same origin / spacing right?</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=""> can you pls help me ?</div><div class="" style=""><div class="" style=""><div style="background-color:transparent;" class="">
<span class="" style=""></span></div><div style="background-color:transparent;" class=""> </div> <div class="" style=""><br clear="none" class="" style=""><br clear="none" class="" style=""></div><div style="display:block;" class=""> <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 face="Arial" class="" style=""> On Tuesday, 17 June 2014 12:59 PM, Nicolas Gallego <<a rel="nofollow" shape="rect" ymailto="mailto:nicgallego@gmail.com" target="_blank" href="mailto:nicgallego@gmail.com" class="" style="">nicgallego@gmail.com</a>> wrote:<br clear="none" class="" style=""> </font> </div> <br clear="none" class="" style=""><br clear="none" class="" style=""> <div class="" style=""><div class="" style="">
<div class="" style=""><div dir="ltr" class="" style=""><div class="" style=""><div class="" style="">Good morning Sindhoor,<br clear="none" class="" style=""><br clear="none" class="" style=""></div>In general itk pipelines process images in the physical space, so that pixelwise operations are between samples on the same physical
position.<br clear="none" class="" style=""></div>Section 4.1.4 of the Software guide [1] and its correspondent example (Image4.cxx) may help you,<br clear="none" class="" style="">
<br clear="none" class="" style="">[1] <a rel="nofollow" shape="rect" target="_blank" href="http://www.itk.org/ItkSoftwareGuide.pdf" class="" style="">http://www.itk.org/ItkSoftwareGuide.pdf</a><br clear="none" class="" style=""></div><div class="" style=""><br clear="all" class="" style=""><div class="" style=""><div dir="ltr" class="" style="">
Nicolás Gallego-Ortiz<br clear="none" class="" style="">Université catholique de Louvain, Belgium<br clear="none" class="" style="">
</div></div>
<br clear="none" class="" style=""><br clear="none" class="" style=""><div class="" style="">2014-06-17 7:28 GMT+02:00 Sindhoor Bhat <span dir="ltr" class="" style=""><<a rel="nofollow" shape="rect" ymailto="mailto:bhatsindhoor@ymail.com" target="_blank" href="mailto:bhatsindhoor@ymail.com" class="" style="">bhatsindhoor@ymail.com</a>></span>:<br clear="none" class="" style="">
<blockquote style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;" class="">
<div 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="">Dear Matt,</div><div class="" style=""><br clear="none" 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="">
I've got error in Geodesic active contour level set segmentation : saying</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="">
itk::ERROR: GeodesicActiveContourLevelSetImageFilter(0000000004AC7160): Inputs do not occupy the same physical space! </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 clear="none" 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="">I searched a lot on solving this error. but none have replied. Can you pls tell how to solve this error?</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'm trying to segment 3D dicom images)</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 clear="none" 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="">thank you.</div></div></div></div><br clear="none" class="" style="">
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