<div dir="ltr"><div><div><div><div>Hi Sindhoor,<br></div>Since you are changing the size of the images via the RegionOfInterestFilter, then you should check that the images provided to your fast marching filter are on the same physical space.<br>
</div>this fragment of code taken form the Examples/Segmentation/FastMarchingImageFilter.cxx<br></div>works because the image region size is that of the BufferedRegion of the reader.<br></div>With the information you have provided that's what I can suggest to check, if anybody has particular experience with this FastMarchingImageFilter that should be taken into account it would be appreciated.<br>
<div class="gmail_extra"><br clear="all"><div><div dir="ltr">Nicolás Gallego-Ortiz<br>Université catholique de Louvain, Belgium<br></div></div>
<br><br><div class="gmail_quote">2014-06-17 14:07 GMT+02:00 Sindhoor Bhat <span dir="ltr"><<a href="mailto:bhatsindhoor@ymail.com" target="_blank">bhatsindhoor@ymail.com</a>></span>:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div><div style="color:#000;background-color:#fff;font-family:times new roman,new york,times,serif;font-size:12pt"><div><span>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">
<span><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"><span>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"><br></div><div style="background-color:transparent"><span style="white-space:pre-wrap"> </span>
OutputImageType:: Pointer image2= sigmoidFilter->GetOutput();</div><div style="background-color:transparent"><span></span></div><div style="background-color:transparent"> image2->Print( std::cout ). </div>
<div style="background-color:transparent"><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">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"> 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></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">
<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">* 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"><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">
<span>Can you pls tell what is wrong?</span></div><div><div class="h5"> <div><br><br></div><div style="display:block"> <div style="font-family:times new roman,new york,times,serif;font-size:12pt"> <div style="font-family:times new roman,new york,times,serif;font-size:12pt">
<div dir="ltr"> <font face="Arial"> On Tuesday, 17 June 2014 2:26 PM, Nicolas Gallego <<a href="mailto:nicgallego@gmail.com" target="_blank">nicgallego@gmail.com</a>> wrote:<br> </font> </div> <br><br> <div><div><div>
<div dir="ltr"><div><div><div><div><div><div><div><div>Hi Sindhoor,<br clear="none"><br clear="none"></div>It's hard to tell. Could you provide a simple code that reproduces your error?<br clear="none"></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">
</div>Refer also to the concepts of regions: there are<br clear="none"></div>LargestPossibleRegion<br clear="none"></div>BufferedRegion<br clear="none"></div>RequestedRegion<br clear="none"><br clear="none"></div>LargestPossibleRegion refers to the whole dataset. Refer to section 13.1 of the software guide for more details.<br clear="none">
</div>I hope that helps,<br clear="none"><div><br clear="all"><div><div dir="ltr">Nicolás Gallego-Ortiz<br clear="none">Université catholique de Louvain, Belgium<br clear="none"></div></div>
<br clear="none"><br clear="none"><div>2014-06-17 10:36 GMT+02:00 Sindhoor Bhat <span dir="ltr"><<a rel="nofollow" shape="rect" href="mailto:bhatsindhoor@ymail.com" target="_blank">bhatsindhoor@ymail.com</a>></span>:<br clear="none">
<div><blockquote style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div><div style="color:#000;background-color:#fff;font-family:times new roman,new york,times,serif;font-size:12pt"><div><span>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">
<span>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"><span>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"><span><br clear="none"></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">
<span>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"><span>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">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">
4.Set seed using fast marching filter.</div><div>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">
<span><br clear="none"></span></div><div style="background-color:transparent"> geodesicActiveContour->SetInput( fastMarching->GetOutput() );</div><div style="background-color:transparent"> geodesicActiveContour->SetFeatureImage( sigmoidFilter->GetOutput() );</div>
<div style="background-color:transparent"><br clear="none"></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">
fastMarching->SetOutputSize(roi_filter->GetOutput()->GetBufferedRegion().GetSize() ); //roi=region of interest<br clear="none"></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">
<br clear="none"></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"> 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"> can you pls help me ?</div><div><div><div style="background-color:transparent">
<span></span></div><div style="background-color:transparent"> </div> <div><br clear="none"><br clear="none"></div><div style="display:block"> <div style="font-family:times new roman,new york,times,serif;font-size:12pt">
<div style="font-family:times new roman,new york,times,serif;font-size:12pt">
<div dir="ltr"> <font face="Arial"> On Tuesday, 17 June 2014 12:59 PM, Nicolas Gallego <<a rel="nofollow" shape="rect" href="mailto:nicgallego@gmail.com" target="_blank">nicgallego@gmail.com</a>> wrote:<br clear="none">
</font> </div> <br clear="none"><br clear="none"> <div><div>
<div><div dir="ltr"><div><div>Good morning Sindhoor,<br clear="none"><br clear="none"></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"></div>Section 4.1.4 of the Software guide [1] and its correspondent example (Image4.cxx) may help you,<br clear="none">
<br clear="none">[1] <a rel="nofollow" shape="rect" href="http://www.itk.org/ItkSoftwareGuide.pdf" target="_blank">http://www.itk.org/ItkSoftwareGuide.pdf</a><br clear="none"></div><div><br clear="all"><div><div dir="ltr">
Nicolás Gallego-Ortiz<br clear="none">Université catholique de Louvain, Belgium<br clear="none">
</div></div>
<br clear="none"><br clear="none"><div>2014-06-17 7:28 GMT+02:00 Sindhoor Bhat <span dir="ltr"><<a rel="nofollow" shape="rect" href="mailto:bhatsindhoor@ymail.com" target="_blank">bhatsindhoor@ymail.com</a>></span>:<br clear="none">
<blockquote style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div><div><div style="color:#000;background-color:#fff;font-family:times new roman,new york,times,serif;font-size:12pt"><div>Dear Matt,</div><div><br clear="none"></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">
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">
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">
<br clear="none"></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">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">(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">
<br clear="none"></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">thank you.</div></div></div></div><br clear="none">
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