Hi Dr. Ludwikow, See inline replies below.
Donna On 07/21/2009 04:59 AM, [email protected] wrote: > Hi, > > I am experiencing some long waiting times while running segmentation > on a pre-packaged Caret 5.61. Today it amounted to 1 h (when ran > caret5), the other day to 20 h (when ran caret5_mesa). One hour is not terribly long; 20 hours is way too long. Was this exactly the same cropped input volume under both scenarios, with only the caret5 vs caret5_mesa difference? If so, I'm very surprised, because I think the only difference is the GL libraries that get linked, and since segmentation is more of a crunch-the-volume thing than something display-intensive, I wouldn't expect much GL involvement. > It is > especially the Auto Error Correction stage that takes long to compute. > Absolutely true. And if you don't mind fixing handles, then turn it off. > Apparently, the same dataset on a Mac takes approx. 20-30 min to be > processed. > This also surprises me -- unless it is a brand new Mac with Xeon processors. > The machine is x86_64 GNU/Linux Ubuntu running 2.6.28-14-generic > #46-Ubuntu SMP kernel. CPU is Intel Xeon X5355 (quad core, @2.66 GHz > each, ca. 5300 BogoMIPS each; model 15, stepping 7). 4 GB RAM, 12 GB > swap. > > top reveals that caret5 is grinding only one of the cores (@100%), > however, I am given to understand that this is only to be expected > ("User's Manual and Tutorial"). > Yeah, the segmentation process is not multi-threaded, and it would probably be hard to make it so. The caret_stats stuff, however, does take advantage of multi-threading (permutation tests). > As I was only introduced to Caret a few days ago, my first suspicion > is that I have been making some silly mistakes. Are there any obvious > and not-so-obvious things to check that would explain such long > computation time? > Here are some suggestions: * Adjust your expectations. Try running Freesurfer on your cases and see how long that takes. (Don't get me wrong; I know it's doing a lot for you.) One hour isn't too bad if it's fixing most of your handles. * Turn off automatic error correction if you can live without it for your purposes (or you don't mind fixing handles). * Don't use caret5_mesa, if all other things were equal when you ran those two trials. * Run multiple segmentations (in separate caret sessions) at a time, to take advantage of multiple threads. Note: I'd put the hemispheres in separate LH and RH subdirectories, to prevent intermediate files from getting trampled on. * Get a Linux box with faster processors. While 2.66 is not slow, I suspect the Mac processors might be faster. * If a segmentation takes longer than a hour, then use a separate Caret session to view the initial segmentation overlaid on the anatomical volume. If the skull or cerebellum is still attached, then this will create quite a feast for the handle fixer; it will take forever; and the end result will be pretty worthless. At that point, you need to figure out how to get rid of the non-cortical junk. > > With kind regards, > Marek Ludwikow > > ---------------------------------------------------------------- > This message was sent using IMP, the Internet Messaging Program. > > > _______________________________________________ caret-users mailing list [email protected] http://brainvis.wustl.edu/mailman/listinfo/caret-users
