Hi Vikram, we are actually looking into the issue of small vessels as part of our research with David. It all depends on the point spread function of your acquisition system and how large is the vessel with respect to it. What we are observing (that is already well known to the field) is that the usual gradient-based deformable models tend to underestimate the size of vessels on MR as they approach the size of the acquisition resolution. The workaround with vmtk is to use the -featureimagetype upwind option in vmtklevelsetsegmentation, which tends to avoid severe underestimation of vessel size at the price of some overestimation.
Having said this, Daniel is right, you really need a ground truth, and if you have a mouse scanner at your disposal the best is to build a simple phantom and scan it at different resolutions. This way you will be sure that you are tuning the segmentation method to your specific acquisition modality. Even talking about MR may not make sense in itself: you need to know what sequence you are using, since, e.g. phase contrast vs contrast-enhanced vs k-centric contrast-enhanced sequences may lead to different signals for the same shape. If you do anything like this it would be great if you let me know about it, as we are very interested in these kinds of issues. Best regards Luca On Feb 8, 2011, at 6:39 PM, Daniel Haehn wrote: > Hi Vikram, > > I did something similar during my Master's thesis. You can find it here > http://www.spl.harvard.edu/publications/item/view/1957 > > You need an expert segmentation as a ground truth and a comparison metric to > do so. > > Cheers, > Daniel > > On Jan 31, 2011, at 6:43 AM, Vikram Mehta wrote: > >> Hello, >> >> I am learning to use vmtk to segment and extract carotid arteries from >> MRI/CT data of mice. >> I am managing to get the surface model but as you know, the diameters of >> mouse arteries are really small and I would like to know if the model that >> VMTK produces is accurate in terms of diameter and other dimensions ? >> >> Is there a way to measure the error (if any) in the diameter of the model >> with respect to the original ? >> >> Thank you in advance >> Vikram. >> >> >> ------------------------------------------------------------------------------ >> Special Offer-- Download ArcSight Logger for FREE (a $49 USD value)! >> Finally, a world-class log management solution at an even better price-free! >> Download using promo code Free_Logger_4_Dev2Dev. Offer expires >> February 28th, so secure your free ArcSight Logger TODAY! >> http://p.sf.net/sfu/arcsight-sfd2d_______________________________________________ >> vmtk-users mailing list >> vmtk-users@lists.sourceforge.net >> https://lists.sourceforge.net/lists/listinfo/vmtk-users > > > > The information contained in this e-mail message is intended only for the > personal and confidential use of the recipient(s) named above. If the reader > of this message is not the intended recipient or an agent responsible for > delivering it to the intended recipient, you are hereby notified that you > have received this document in error and that any review, dissemination, > distribution, or copying of this message is strictly prohibited. If you have > received this communication in error, please notify us immediately by e-mail, > and delete the original message. > > ------------------------------------------------------------------------------ > The ultimate all-in-one performance toolkit: Intel(R) Parallel Studio XE: > Pinpoint memory and threading errors before they happen. > Find and fix more than 250 security defects in the development cycle. > Locate bottlenecks in serial and parallel code that limit performance. > http://p.sf.net/sfu/intel-dev2devfeb > _______________________________________________ > vmtk-users mailing list > vmtk-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/vmtk-users ------------------------------------------------------------------------------ The ultimate all-in-one performance toolkit: Intel(R) Parallel Studio XE: Pinpoint memory and threading errors before they happen. Find and fix more than 250 security defects in the development cycle. Locate bottlenecks in serial and parallel code that limit performance. http://p.sf.net/sfu/intel-dev2devfeb _______________________________________________ vmtk-users mailing list vmtk-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/vmtk-users
