<html><head><meta http-equiv="Content-Type" content="text/html charset=windows-1252"><base href="x-msg://1415/"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">If you running some variant of linux you should be able to limit the memory used for a process. This may give you better behavior. Here may be a place to start:<div><br></div><div><a href="http://stackoverflow.com/questions/4651234/linux-process-memory-limit">http://stackoverflow.com/questions/4651234/linux-process-memory-limit</a></div><div><br></div><div>Brad</div><div><br></div><div><div>On Dec 11, 2013, at 1:45 PM, Ben Alpert <<a href="mailto:balpert@numira.com">balpert@numira.com</a>> wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div lang="EN-US" link="blue" vlink="purple" style="font-family: Helvetica; font-size: medium; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: -webkit-auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; "><div class="WordSection1" style="page: WordSection1; "><div style="margin: 0in 0in 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125); ">Thanks for your help. I think breaking up the image into smaller blocks and running the filter on those is the way to go. The main problem is that I need to be able catch an exception when memory fails to allocate in order to then break up the image. I can’t take a chance of having my system freeze if the system happens to be low on memory. Do you happen to know why an exception isn’t thrown, and how can I fix this?<o:p></o:p></span></div><div style="margin: 0in 0in 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125); "> </span></div><div style="margin: 0in 0in 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125); ">Thanks,<o:p></o:p></span></div><div style="margin: 0in 0in 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125); ">Ben<o:p></o:p></span></div><div style="margin: 0in 0in 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125); "> </span></div><div><div style="border-style: solid none none; border-top-width: 1pt; border-top-color: rgb(181, 196, 223); padding: 3pt 0in 0in; "><div style="margin: 0in 0in 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; "><b><span style="font-size: 10pt; font-family: Tahoma, sans-serif; ">From:</span></b><span style="font-size: 10pt; font-family: Tahoma, sans-serif; "><span class="Apple-converted-space"> </span>Bradley Lowekamp [mailto:brad@<a href="http://lowekamp.net" style="color: purple; text-decoration: underline; ">lowekamp.net</a>]<span class="Apple-converted-space"> </span><br><b>Sent:</b><span class="Apple-converted-space"> </span>Monday, December 09, 2013 12:41 PM<br><b>To:</b><span class="Apple-converted-space"> </span>Ben Alpert<br><b>Cc:</b><span class="Apple-converted-space"> </span><a href="mailto:insight-users@itk.org" style="color: purple; text-decoration: underline; ">insight-users@itk.org</a><br><b>Subject:</b><span class="Apple-converted-space"> </span>Re: [Insight-users] Vesselness Memory Issue<o:p></o:p></span></div></div></div><div style="margin: 0in 0in 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; "><o:p> </o:p></div><div style="margin: 0in 0in 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; ">Hello,<o:p></o:p></div><div><div style="margin: 0in 0in 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; "><o:p> </o:p></div></div><div><div style="margin: 0in 0in 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; ">You system lockup is likely due to memory exhaustion, and excessive thrashing. System lockup it typical of when running you of memory for an task.<o:p></o:p></div></div><div><div style="margin: 0in 0in 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; "><o:p> </o:p></div></div><div><div style="margin: 0in 0in 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; ">I had a version of the MultiScaleHessian that was streamable. I haven't used it for a while not, and don't know what the state of it is after ITKv4.<o:p></o:p></div></div><div><div style="margin: 0in 0in 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; "><a href="http://review.source.kitware.com/#/c/890/" style="color: purple; text-decoration: underline; ">http://review.source.kitware.com/#/c/890/</a><o:p></o:p></div></div><div><div style="margin: 0in 0in 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; "><o:p> </o:p></div></div><div><div style="margin: 0in 0in 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; ">You have a couple other options:<o:p></o:p></div></div><div><div style="margin: 0in 0in 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; "><o:p> </o:p></div></div><div><div style="margin: 0in 0in 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; ">1) Find smaller regions of interest. That is just don't run on the whole image at once.<o:p></o:p></div></div><div><div style="margin: 0in 0in 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; ">2) For each scale stream your metric to disk. This is the way I recently did it. I was able to batch each scale out to a cluster node. And them perform on analysis on the scalar images in SimpleITK.<o:p></o:p></div></div><div><div style="margin: 0in 0in 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; "><o:p> </o:p></div></div><div><div style="margin: 0in 0in 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; ">Those on my quick suggestions.<o:p></o:p></div></div><div><div style="margin: 0in 0in 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; "><o:p> </o:p></div></div><div><div style="margin: 0in 0in 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; ">Good luck,<o:p></o:p></div></div><div><div style="margin: 0in 0in 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; ">Brad<o:p></o:p></div></div><div><div style="margin: 0in 0in 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; "><o:p> </o:p></div></div><div><div style="margin: 0in 0in 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; "><o:p> </o:p></div><div><div><div style="margin: 0in 0in 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; ">On Dec 9, 2013, at 2:20 PM, Ben Alpert <<a href="mailto:balpert@numira.com" style="color: purple; text-decoration: underline; ">balpert@numira.com</a>> wrote:<o:p></o:p></div></div><div style="margin: 0in 0in 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; "><br><br><o:p></o:p></div><div><div><div style="margin: 0in 0in 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="font-size: 11pt; font-family: Calibri, sans-serif; ">Hi,<o:p></o:p></span></div></div><div><div style="margin: 0in 0in 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="font-size: 11pt; font-family: Calibri, sans-serif; "> <o:p></o:p></span></div></div><div><div style="margin: 0in 0in 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="font-size: 11pt; font-family: Calibri, sans-serif; ">I have seen a few threads on this topic but I am still not sure what the best approach is. I am trying to enhance vessels using the MultiScaleHessianBasedMeasureImageFilter and Hessian3DToVesselnessMeasureImageFilter framework. When running the filters on a large enough volume, my system locks up, so there seems to be some exception handling issue since I would at least expect an error message in this case.<o:p></o:p></span></div></div><div><div style="margin: 0in 0in 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="font-size: 11pt; font-family: Calibri, sans-serif; "> <o:p></o:p></span></div></div><div><div style="margin: 0in 0in 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="font-size: 11pt; font-family: Calibri, sans-serif; ">I understand that the HessianRecursiveGaussianImageFilter is not streamable and I have seen that a discrete version is available (<a href="https://github.com/blowekamp/itkLocalDiscreteHessian" style="color: purple; text-decoration: underline; "><span style="color: purple; ">https://github.com/blowekamp/itkLocalDiscreteHessian</span></a>), but I am not sure how to integrate it with the MultiScaleHessian framework. Did anyone have any experience with this?<o:p></o:p></span></div></div><div><div style="margin: 0in 0in 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="font-size: 11pt; font-family: Calibri, sans-serif; "> <o:p></o:p></span></div></div><div><div style="margin: 0in 0in 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="font-size: 11pt; font-family: Calibri, sans-serif; ">Also, other than for visualization/UI purposes, is there any advantage in using tubetk, as it is essentially built on itk?<o:p></o:p></span></div></div><div><div style="margin: 0in 0in 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="font-size: 11pt; font-family: Calibri, sans-serif; "> <o:p></o:p></span></div></div><div><div style="margin: 0in 0in 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="font-size: 11pt; font-family: Calibri, sans-serif; ">Any help is appreciated.<o:p></o:p></span></div></div><div><div style="margin: 0in 0in 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="font-size: 11pt; font-family: Calibri, sans-serif; ">Thanks,<o:p></o:p></span></div></div><div><div style="margin: 0in 0in 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="font-size: 11pt; font-family: Calibri, sans-serif; ">Ben<o:p></o:p></span></div></div><div style="margin: 0in 0in 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="font-size: 13.5pt; font-family: Helvetica, sans-serif; ">_____________________________________<br>Powered by<span class="apple-converted-space"> </span><a href="http://www.kitware.com" style="color: purple; text-decoration: underline; "><span style="color: purple; ">www.kitware.com</span></a><br><br>Visit other Kitware open-source projects at<br><a href="http://www.kitware.com/opensource/opensource.html" style="color: purple; text-decoration: underline; "><span style="color: purple; ">http://www.kitware.com/opensource/opensource.html</span></a><br><br>Kitware offers ITK Training Courses, for more information visit:<br><a href="http://www.kitware.com/products/protraining.php" style="color: purple; text-decoration: underline; "><span style="color: purple; ">http://www.kitware.com/products/protraining.php</span></a><br><br>Please keep messages on-topic and check the ITK FAQ at:<br><a href="http://www.itk.org/Wiki/ITK_FAQ" style="color: purple; text-decoration: underline; "><span style="color: purple; ">http://www.itk.org/Wiki/ITK_FAQ</span></a><br><br>Follow this link to subscribe/unsubscribe:<br><a href="http://www.itk.org/mailman/listinfo/insight-users" style="color: purple; text-decoration: underline; "><span style="color: purple; ">http://www.itk.org/mailman/listinfo/insight-users</span></a><o:p></o:p></span></div></div></div><div style="margin: 0in 0in 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; "><o:p> </o:p></div></div></div></div></blockquote></div><br></body></html>