Dear Vikram, sorry that you didn't get a reply yet, I'm currently abroad for work. vmtk doesn't have an internal memory setting (like for example with ImageJ). It uses whatever memory the system can allocate. You are on Red Hat Enterprise, right? I assume 64 bit (if it's 32 bit then you won't be able to allocate sufficient memory regardless how much physical memory you have)
Usually vmtklevelsetsegmentation consumes quite a lot of memory, but simply reading the images shouldn't. Can you read the images using vmtkimagereader or visualize them with vmtkimageviewer or you get a segmentation fault even in this case? (from your message it's probably the latter case). What exact command are you using to read the data? Reducing the size of the dataset is probably the way to go. If you can read it with vmtkimagereader, then of course you can use vmtkimagevoiselector, but if you can't, then try removing the first and last slices. Apparently the slices are not sorted by filename, so you should rely on a software to sort them out before you reduce the dataset. You could try with OsiriX if you have a Mac around, or with this Dicom Browser: http://www.nitrc.org/projects/dicom_browser/ I hope this helps Luca On Aug 18, 2011, at 12:04 PM, Vikram Mehta wrote: > Hello, > > I have been using VMTK for segmentation purposes from CT scan datasets. I > recenly received a high resolution dataset (35 micron) to have a better > contrast and hence better segmentation and the size of the dataset is around > 800mb. > When I tried to load it in VMTK, it gives me a segmentation fault error. > > So I tried reducing the size of the folder by just dividing the images into 2 > folders of 400 mb each and now they open but the images don´t make much sense. > I would like to know if there is a way around this problem. Is this due to > low internal memory of VMTK ? Is there a way of increasing it ? > > Please let me know. It would be very helpful. > > Thanking you > Vikram. > > ------------------------------------------------------------------------------ > Get a FREE DOWNLOAD! and learn more about uberSVN rich system, > user administration capabilities and model configuration. Take > the hassle out of deploying and managing Subversion and the > tools developers use with it. > http://p.sf.net/sfu/wandisco-d2d-2_______________________________________________ > vmtk-users mailing list > vmtk-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/vmtk-users ------------------------------------------------------------------------------ EMC VNX: the world's simplest storage, starting under $10K The only unified storage solution that offers unified management Up to 160% more powerful than alternatives and 25% more efficient. Guaranteed. http://p.sf.net/sfu/emc-vnx-dev2dev _______________________________________________ vmtk-users mailing list vmtk-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/vmtk-users
