<html xmlns:v="urn:schemas-microsoft-com:vml" xmlns:o="urn:schemas-microsoft-com:office:office" xmlns:w="urn:schemas-microsoft-com:office:word" xmlns:m="http://schemas.microsoft.com/office/2004/12/omml" xmlns="http://www.w3.org/TR/REC-html40"><head><META HTTP-EQUIV="Content-Type" CONTENT="text/html; charset=us-ascii"><meta name=Generator content="Microsoft Word 14 (filtered medium)"><style><!--
/* Font Definitions */
@font-face
{font-family:Calibri;
panose-1:2 15 5 2 2 2 4 3 2 4;}
@font-face
{font-family:Tahoma;
panose-1:2 11 6 4 3 5 4 4 2 4;}
/* Style Definitions */
p.MsoNormal, li.MsoNormal, div.MsoNormal
{margin:0in;
margin-bottom:.0001pt;
font-size:11.0pt;
font-family:"Calibri","sans-serif";}
a:link, span.MsoHyperlink
{mso-style-priority:99;
color:blue;
text-decoration:underline;}
a:visited, span.MsoHyperlinkFollowed
{mso-style-priority:99;
color:purple;
text-decoration:underline;}
span.EmailStyle17
{mso-style-type:personal;
font-family:"Calibri","sans-serif";
color:windowtext;}
span.EmailStyle18
{mso-style-type:personal-reply;
font-family:"Calibri","sans-serif";
color:#1F497D;}
.MsoChpDefault
{mso-style-type:export-only;
font-size:10.0pt;}
@page WordSection1
{size:8.5in 11.0in;
margin:1.0in 1.0in 1.0in 1.0in;}
div.WordSection1
{page:WordSection1;}
--></style><!--[if gte mso 9]><xml>
<o:shapedefaults v:ext="edit" spidmax="1026" />
</xml><![endif]--><!--[if gte mso 9]><xml>
<o:shapelayout v:ext="edit">
<o:idmap v:ext="edit" data="1" />
</o:shapelayout></xml><![endif]--></head><body lang=EN-US link=blue vlink=purple><div class=WordSection1><p class=MsoNormal><span style='color:#1F497D'>Anybody? Any ideas as to how I might debug this problem?<o:p></o:p></span></p><p class=MsoNormal><span style='color:#1F497D'><o:p> </o:p></span></p><p class=MsoNormal><span style='color:#1F497D'>Thanks<o:p></o:p></span></p><p class=MsoNormal><span style='color:#1F497D'><o:p> </o:p></span></p><p class=MsoNormal><span style='color:#1F497D'> -- Scott<o:p></o:p></span></p><p class=MsoNormal><span style='color:#1F497D'><o:p> </o:p></span></p><div><div style='border:none;border-top:solid #B5C4DF 1.0pt;padding:3.0pt 0in 0in 0in'><p class=MsoNormal><b><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'>From:</span></b><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'> insight-users-bounces@itk.org [mailto:insight-users-bounces@itk.org] <b>On Behalf Of </b>Scott Johnson<br><b>Sent:</b> Tuesday, January 29, 2013 2:01 PM<br><b>To:</b> itk (Insight-users@itk.org)<br><b>Subject:</b> [Insight-users] ConnectedThresholdImageFilter Seed Problems<o:p></o:p></span></p></div></div><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>Hello,<o:p></o:p></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>I have been attempting to use ConnectedThresholdImageFilter to identify a feature in some images. I’m puzzled because it seems that the mask generated by ConnectedThresholdImageFilter works as expected the first time, but then seems to behave almost the same as the ThresholdImageFilter, in subsequent executions. I have verified that the seed points are still there. I have also tried to build my instance of ConnectedThresholdImageFilter from scratch each time I want to execute it. The behavior is the same either way.<o:p></o:p></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>I have verified that my seed positions are valid. I will attach an image with a small cross showing one of the seed positions and the mask generated by ConnectedThresholdImageFilter. The seed point is within the small blob near the left side of the image, and I have verified that all of the seeds are within that same feature, and the feature is not connected to other parts of the mask.<o:p></o:p></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>I am using ITK 4.2 on a Windows 7 64x platform, running under VS 2008.<o:p></o:p></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>When I create the ConnectedThresholdImageFilter I set the following attributes of the new instance:<o:p></o:p></p><p class=MsoNormal>(This code is only partial but should give you an idea of what I’m doing.)<o:p></o:p></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal style='text-autospace:none'><span style='font-size:10.0pt;font-family:"Courier New"'> <span style='color:blue'>typedef</span> itk::Image<<span style='color:blue'>short</span>, 3> DICOMImageType;<o:p></o:p></span></p><p class=MsoNormal style='text-autospace:none'><span style='font-size:10.0pt;font-family:"Courier New"'> <span style='color:blue'>typedef</span> DICOMImageType::Pointer DICOMImagePointer;<o:p></o:p></span></p><p class=MsoNormal style='text-autospace:none'><span style='font-size:10.0pt;font-family:"Courier New"'> <span style='color:blue'>typedef</span> itk::Image<<span style='color:blue'>unsigned</span> <span style='color:blue'>char</span>, 3> MaskImageType;<o:p></o:p></span></p><p class=MsoNormal style='text-autospace:none'><span style='font-size:10.0pt;font-family:"Courier New"'> <span style='color:blue'>typedef</span> MaskImageType::Pointer MaskImagePointer;<o:p></o:p></span></p><p class=MsoNormal style='text-autospace:none'><span style='font-size:10.0pt;font-family:"Courier New"'><o:p> </o:p></span></p><p class=MsoNormal style='text-autospace:none'><span style='font-size:10.0pt;font-family:"Courier New"'> <span style='color:blue'>typedef</span> itk::ConnectedThresholdImageFilter<DICOMImageType, MaskImageType><o:p></o:p></span></p><p class=MsoNormal style='text-autospace:none'><span style='font-size:10.0pt;font-family:"Courier New"'> SeedGrowerType;<o:p></o:p></span></p><p class=MsoNormal style='text-autospace:none'><span style='font-size:10.0pt;font-family:"Courier New"'> <span style='color:blue'>typedef</span> SeedGrowerType::Pointer SeedGrowerPointer;<o:p></o:p></span></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal style='margin-left:.5in;text-autospace:none'><span style='font-size:10.0pt;font-family:"Courier New";color:blue'>#define</span><span style='font-size:10.0pt;font-family:"Courier New"'> LOW_THRESHOLD 100<o:p></o:p></span></p><p class=MsoNormal style='margin-left:.5in;text-autospace:none'><span style='font-size:10.0pt;font-family:"Courier New";color:blue'>#define</span><span style='font-size:10.0pt;font-family:"Courier New"'> HIGH_THRESHOLD 4095<o:p></o:p></span></p><p class=MsoNormal style='margin-left:.5in;text-autospace:none'><span style='font-size:10.0pt;font-family:"Courier New";color:blue'>#define</span><span style='font-size:10.0pt;font-family:"Courier New"'> REPLACE_VALUE 255<o:p></o:p></span></p><p class=MsoNormal style='text-autospace:none'><span style='font-size:10.0pt;font-family:"Courier New"'><o:p> </o:p></span></p><p class=MsoNormal style='text-autospace:none'><span style='font-size:10.0pt;font-family:"Courier New"'> _seedGrower = SeedGrowerType::New();<o:p></o:p></span></p><p class=MsoNormal style='text-autospace:none'><span style='font-size:10.0pt;font-family:"Courier New"'> // _smoothDiff is the result of convolving an image with<o:p></o:p></span></p><p class=MsoNormal style='text-autospace:none'><span style='font-size:10.0pt;font-family:"Courier New"'> // a 3x3 kernel and the output image is a short.<o:p></o:p></span></p><p class=MsoNormal style='text-autospace:none'><span style='font-size:10.0pt;font-family:"Courier New"'> _seedGrower->SetInput(_smoothDiff->GetOutput());<o:p></o:p></span></p><p class=MsoNormal style='text-autospace:none'><span style='font-size:10.0pt;font-family:"Courier New"'> // The AddSeeds method invokes _seedGrower->AddSeed to add<o:p></o:p></span></p><p class=MsoNormal style='text-autospace:none'><span style='font-size:10.0pt;font-family:"Courier New"'> // seeds to the instance.<o:p></o:p></span></p><p class=MsoNormal style='text-autospace:none'><span style='font-size:10.0pt;font-family:"Courier New"'> AddSeeds(debugStream);<o:p></o:p></span></p><p class=MsoNormal style='text-autospace:none'><span style='font-size:10.0pt;font-family:"Courier New"'> _seedGrower->SetLower(LOW_THRESHOLD);<o:p></o:p></span></p><p class=MsoNormal style='text-autospace:none'><span style='font-size:10.0pt;font-family:"Courier New"'> _seedGrower->SetUpper(HIGH_THRESHOLD);<o:p></o:p></span></p><p class=MsoNormal style='text-autospace:none'><span style='font-size:10.0pt;font-family:"Courier New"'> _seedGrower->SetReplaceValue(REPLACE_VALUE);<o:p></o:p></span></p><p class=MsoNormal style='text-autospace:none'><span style='font-size:10.0pt;font-family:"Courier New"'> _seedGrower->Update();<o:p></o:p></span></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>The mask in the attached image is the result of _seedGrower->GetOutput(). The mask image has a pixel type of unsigned char.<o:p></o:p></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>I have tried both FaceConnectivity and FullConnectivity via the SetConnectivity method, but it made no difference. I have also dumped the output of _smoothDiff and it makes sense.<o:p></o:p></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>I need to determine why the ConnectedThresholdImageFilter is not always paying attention to my seed positions. If it is paying attention to my seed points then the seed growth isn’t stopping at the end of the feature. I’d appreciate any pointers anyone can provide.<o:p></o:p></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>Thanks<o:p></o:p></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal> -- Scott<o:p></o:p></p><p class=MsoNormal><o:p> </o:p></p></div></body></html>