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</o:shapelayout></xml><![endif]--></head><body lang=DE-AT link=blue vlink=purple><div class=WordSection1><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>Hi Sergio Vera,<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'><o:p> </o:p></span></p><p class=MsoNormal><span lang=EN-GB style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>Thank you for your response. The image resolution is 3µm. The extent is approx 3300*3300*1300.<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-GB style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>I will have a look at the recommendations in the link.<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-GB style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'><o:p> </o:p></span></p><p class=MsoNormal><span lang=EN-GB style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>As you said Hessian calculation might be a problem. I was thinking of breaking the image into smaller region of interest <o:p></o:p></span></p><p class=MsoNormal><span lang=EN-GB style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>and calculate the hessian, then apply my function in the region and store the result in segmented image(equal to size of input image) in the respective region.<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-GB style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>This was just an idea ... Is this possible ? Will this lead to the changes in the hessian calculation at the end which is shared with next region?<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-GB style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'><o:p> </o:p></span></p><p class=MsoNormal><span lang=EN-GB style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>Thank you,<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-GB style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>Regards,<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-GB style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>Kana<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-GB style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'><o:p> </o:p></span></p><div style='border:none;border-top:solid #B5C4DF 1.0pt;padding:3.0pt 0cm 0cm 0cm'><p class=MsoNormal><b><span lang=EN-US style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'>From:</span></b><span lang=EN-US style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'> Sergio Vera [mailto:sergio.vera@alma3d.com] <br><b>Sent:</b> 26 November 2010 09:34<br><b>To:</b> Arunachalam Kana<br><b>Cc:</b> insight-users@itk.org<br><b>Subject:</b> Re: [Insight-users] Memory issue<o:p></o:p></span></p></div><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>Without knowing the exact image resolution/size, I would expect difficulties with the hessian at least: on a hessian image each pixel is a 3x3 double matrix... just multiply...and add intermediate images inbetween the pipeline, other procesess..<o:p></o:p></p><div><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><o:p> </o:p></p></div><div><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>You may certainly experiment some memory problems. Check this thread for tips related to memory and speed optimizations within ITK: <a href="http://old.nabble.com/Guidelines-for-speed-and-memory-footprint-optimization-td30178329.html">http://old.nabble.com/Guidelines-for-speed-and-memory-footprint-optimization-td30178329.html</a><o:p></o:p></p></div><div><div><p class=MsoNormal style='mso-margin-top-alt:auto;margin-bottom:12.0pt'><o:p> </o:p></p><div><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>On Thu, Nov 25, 2010 at 5:54 PM, Arunachalam Kana <<a href="mailto:Kana.Arunachalam@fh-wels.at" target="_blank">Kana.Arunachalam@fh-wels.at</a>> wrote:<o:p></o:p></p><div><div><p>Hi ITK Users,<o:p></o:p></p><p> <o:p></o:p></p><p><span lang=EN-GB>Situation: I have 32Gb unsigned short image and I use a 64bit machine, with linux, and my RAM size is 64Gb. I would like to apply the following itk algorithm:</span><o:p></o:p></p><p><span lang=EN-GB>Step1: Original image -> Anisotropic diffusion image filter -> smoothed image</span><o:p></o:p></p><p><span lang=EN-GB> </span><o:p></o:p></p><p><span lang=EN-GB>Step 2: Own filter: I calculate the hessian for the input image. I use the hessian image and the input image to segment and produce an output image.</span><o:p></o:p></p><p><span lang=EN-GB>Smoothed image -> hessianrecurssivegaussianimagefilter-> smoothed image + hessian image ->segmentation function -> segmented image</span><o:p></o:p></p><p><span lang=EN-GB> </span><o:p></o:p></p><p><span lang=EN-GB>Step 3: Segmented image -> 3dbinarythinning -> thinned image.</span><o:p></o:p></p><p><span lang=EN-GB> </span><o:p></o:p></p><p><span lang=EN-GB>After every step the output image will be save to local hard disk.</span><o:p></o:p></p><p><span lang=EN-GB> </span><o:p></o:p></p><p><span lang=EN-GB>Questions:</span><o:p></o:p></p><p style='margin-left:18.0pt'><span lang=EN-GB>1.</span><span lang=EN-GB style='font-size:7.0pt'> </span><span lang=EN-GB>Will there be any memory problem in application of anisotropic diffusion filter, hessian filter and 3dbinarythinning? </span><o:p></o:p></p><p style='margin-left:18.0pt'><span lang=EN-GB>2.</span><span lang=EN-GB style='font-size:7.0pt'> </span><span lang=EN-GB>If the answer is yes to the above question. How can i solve it? </span><o:p></o:p></p><p><span lang=EN-GB>Thank you,</span><o:p></o:p></p><p><span lang=EN-GB>Regards,</span><o:p></o:p></p><p style='margin:0cm;margin-bottom:.0001pt'>Kana Arunachalam Kannappan<o:p></o:p></p><p style='margin:0cm;margin-bottom:.0001pt'>Research Associate<o:p></o:p></p><p style='margin:0cm;margin-bottom:.0001pt'>FH OÖ Forschungs & Entwicklungs GmbH<o:p></o:p></p><p style='margin:0cm;margin-bottom:.0001pt'>Stelzhamer Strasse 23,<o:p></o:p></p><p style='margin:0cm;margin-bottom:.0001pt'>4600 Wels,<o:p></o:p></p><p style='margin:0cm;margin-bottom:.0001pt'>Austria.<o:p></o:p></p><p style='margin:0cm;margin-bottom:.0001pt'>Phone: +43 (0)7242 72811 -4420<o:p></o:p></p><p style='margin:0cm;margin-bottom:.0001pt'><a href="mailto:kana.arunachalam@fh-wels.at" target="_blank">kana.arunachalam@fh-wels.at</a><o:p></o:p></p><p style='margin:0cm;margin-bottom:.0001pt'><a href="http://www.fh-ooe.at" target="_blank">www.fh-ooe.at</a>; <a href="http://www.3dct.at" target="_blank">www.3dct.at</a><o:p></o:p></p><p> <o:p></o:p></p></div></div><p class=MsoNormal style='margin-bottom:12.0pt'><br>_____________________________________<br>Powered by <a href="http://www.kitware.com" target="_blank">www.kitware.com</a><br><br>Visit other Kitware open-source projects at<br><a href="http://www.kitware.com/opensource/opensource.html" target="_blank">http://www.kitware.com/opensource/opensource.html</a><br><br>Kitware offers ITK Training Courses, for more information visit:<br><a href="http://www.kitware.com/products/protraining.html" target="_blank">http://www.kitware.com/products/protraining.html</a><br><br>Please keep messages on-topic and check the ITK FAQ at:<br><a href="http://www.itk.org/Wiki/ITK_FAQ" target="_blank">http://www.itk.org/Wiki/ITK_FAQ</a><br><br>Follow this link to subscribe/unsubscribe:<br><a href="http://www.itk.org/mailman/listinfo/insight-users" target="_blank">http://www.itk.org/mailman/listinfo/insight-users</a><o:p></o:p></p></div><p class=MsoNormal><br><br clear=all><br>-- <br>Sergio Vera<br><br> Alma IT Systems<br> C/ Vilana, 4B, 4º 1ª<br> 08022 Barcelona<br> T. (+34) 932 380 592<br> <a href="http://www.alma3d.com" target="_blank">www.alma3d.com</a><o:p></o:p></p></div></div></div></body></html>