Sorry, visual artifacts- yes (still there), crashing/freezing- no (but I've been trying hard). It's only been about an hour since the update, I'll keep you posted. So, should I worry about the artifacts affecting output? If I scroll through the slices long enough, they eventually all disappear.
-Derin > OK, so since you updated the graphics driver, you've had no problems > with either the visual artifacts or the crashing/freezing? If there > have been no problems, we'll assume the graphics driver fixed > it. Otherwise, let us know. > > On Tue, Aug 29, 2006 at 01:24:09PM -0500, Derin Cobia wrote: >> Bruce, >> >> No, I processed all of them the same way (converted files, -autorecon1, >> etc). The scan quality differs among them, but I tossed the really bad >> ones. Here is the xdebug file. Also, is what I'm seeing in this slice >> (see attached jpg) something to worry about? If I scroll through other >> slices, then come back to it, the artifacts are gone. This happens >> randomly on various slices on some of the subjects, but it never stays. >> >> I have updated the drivers for the video card, and haven't had any >> issues >> (yet). I'll keep my eye on it. Thanks for your help. >> >> -Derin >> >> > were these processed any differently? The .xdebug_tkmedit should be in >> pwd >> > wherever you ran it from. >> > >> > Bruce >> > >> > >> > On Tue, 29 Aug 2006, Derin Cobia >> > wrote: >> > >> >> Kevin- >> >> Yeah, either way. In my "infinite" wisdom I thought that scrolling >> >> slower >> >> would help, but not so. >> >> >> >> Nick- >> >> I'm unable to locate a .xdebug_tkmedit file in either the freesurfer >> or >> >> subjects directory. Would it be somewhere else? It looks like we're >> >> using the 1.0-8178 Nvidia driver for our Quadro FX card, but their >> site >> >> shows a 1.0-8762 as the latest. I'll see if we can update it today, >> >> maybe >> >> that will help. >> >> >> >> On the side... why are my intensity values "infinite" for the >> following >> >> subject? I've briefly checked brainmask.mgz, and differing >> intensities >> >> appear. Any ideas? Thanks. >> >> >> >> -Derin >> >> >> >> #-------------------------------------------- >> >> [EMAIL PROTECTED] WM Segmentation Mon Aug 28 04:00:48 CDT 2006 >> >> >> >> mri_segment brain.mgz wm.seg.mgz >> >> >> >> doing initial intensity segmentation... >> >> using local statistics to label ambiguous voxels... >> >> computing class statistics for intensity windows... >> >> WM: nan +- nan [100000.0 --> -100000.0] >> >> GM: nan +- nan [100000.0 --> -100000.0] >> >> mri_segment: class statistics not finite - check input volume! >> >> Linux gizmo 2.6.9-11.ELsmp #1 SMP Wed Jun 8 17:54:20 CDT 2005 i686 >> i686 >> >> i386 GNU/Linux >> >> >> >> recon-all exited with ERRORS at Mon Aug 28 04:00:54 CDT 2006 >> >> >> >> >> >>> Hm, I can't reproduce this. >> >>> >> >>> So, you load up a volume, and repeatedly press an arrow key to >> scroll >> >>> through the slices? Or hold the button down? >> >>> >> >>> On Mon, Aug 28, 2006 at 11:16:49AM -0500, Derin Cobia wrote: >> >>>> I've been experiencing some crashes/freezing using tkmedit lately, >> and >> >>>> have been able to reproduce it pretty reliably. It occurs when I >> >>>> scroll >> >>>> through the slices of the subject either using the arrows keys or >> >>>> clicking >> >>>> through on the toolbar. It happens when viewing a variety of >> volumes >> >>>> (brainmask, T1, etc), and from a variety of perspectives (coronal, >> >>>> sagittal, etc); it also happens on different subjects as well. >> This >> >>>> occurs no matter what workstation I use in the lab (networked >> >>>> environment). My X freezes up as well as the keyboard, but the >> mouse >> >>>> doesn't. I used to be able to restart my X remotely, but now >> tkmedit >> >>>> locks up so bad I have to reboot. Any ideas? >> >>>> >> >>>> Dell Precision 670 Workstations >> >>>> CentOS 4.1 (32-bit) >> >>>> >> >>>> -------- freesurfer-Linux-centos4-stable-pub-v3.0.3 -------- >> >>>> Setting up environment for FreeSurfer/FS-FAST (and FSL) >> >>>> FREESURFER_HOME /pkg/brainmap/freesurfer >> >>>> FSFAST_HOME /pkg/brainmap/freesurfer/fsfast >> >>>> SUBJECTS_DIR /disk/k2/freesurfer/neuromorph_v1_flash/ >> >>>> FUNCTIONALS_DIR /pkg/brainmap/freesurfer/sessions >> >>>> MINC_BIN_DIR /pkg/brainmap/freesurfer/mni/bin >> >>>> MINC_LIB_DIR /pkg/brainmap/freesurfer/mni/lib >> >>>> PERL5LIB /pkg/brainmap/freesurfer/mni/lib/perl5/5.8.0 >> >>>> GSL_DIR /pkg/brainmap/freesurfer/lib/gsl >> >>>> QTDIR /usr/lib/qt-3.3 >> >>>> TCLLIBPATH /pkg/brainmap/freesurfer/lib/tcltktixblt/lib >> >>>> FSL_DIR /pkg/brainmap/freesurfer/fsl >> >>>> >> >>>> [EMAIL PROTECTED] ~]$ which tkmedit >> >>>> /pkg/brainmap/freesurfer/bin//tkmedit >> >>>> >> >>>> cd /disk/k2/freesurfer/neuromorph_v1_flash/ >> >>>> >> >>>> Thanks in advance. >> >>> >> >>> >> >>> -- >> >>> Kevin Teich >> >>> >> >> >> >> _______________________________________________ >> >> Freesurfer mailing list >> >> Freesurfer@nmr.mgh.harvard.edu >> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> >> >> >> >> > >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> > > -- > Kevin Teich > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
