[Freesurfer] tkmedit crashes/freezes
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. -Derin ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] tkmedit crashes/freezes
Derin, Does the file .xdebug_tkmedit show any error messages after a lock-up occurs? If so, can you send that file to me? Another possibility is that the graphics driver may need to be updated. Do you have an NVIDIA card? Nick > 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. > > -Derin > > ___ > 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
Re: [Freesurfer] tkmedit crashes/freezes
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
Re: [Freesurfer] tkmedit crashes/freezes
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 [10.0 --> -10.0] GM: nan +- nan [10.0 --> -10.0] 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
Re: [Freesurfer] tkmedit crashes/freezes
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 [10.0 --> -10.0] GM: nan +- nan [10.0 --> -10.0] 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
Re: [Freesurfer] tkmedit crashes/freezes
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 [10.0 --> -10.0] >> GM: nan +- nan [10.0 --> -10.0] >> 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
Re: [Freesurfer] tkmedit crashes/freezes
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 [10.0 --> -10.0] > >> GM: nan +- nan [10.0 --> -10.0] > >> 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.ed
Re: [Freesurfer] tkmedit crashes/freezes
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 [10.0 --> -10.0] >> >> GM: nan +- nan [10.0 --> -10.0] >> >> 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 >> >>> >> >> >> >> ___
Re: [Freesurfer] tkmedit crashes/freezes
Not sure what would give you nans though. Can you find a voxel with a nan in it and see at what point it gets created (e.g. orig.mgz, T1.mgz, etc..) no attachment... Bruce On Tue, 29 Aug 2006, 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 [10.0 --> -10.0] GM: nan +- nan [10.0 --> -10.0] 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
