Re: [caret-users] crash of X KDE session
Hi Donna, I have tried to use File: Open Volume Anatomy and Open Volume Functional on: image.hdr image.HEAD image.nii as you suggested, but unfortunately they all cause the X session to crash. Thank you for you help! Best, Marco Donna Dierker wrote: Marco, Does the problem occur when you use File: Open Volume Anatomy (or functional) File to open the same file? If so, does it occur if you convert the file to NIfTI and/or AFNI? I'm guessing it will (e.g., suggesting a display issue, rather than a file I/O issue), but it helps to be sure. If you have trouble converting to another file format, then upload the file here, and I'll provide you the converted version: http://pulvinar.wustl.edu/cgi-bin/upload.cgi On 11/30/2006 04:08 AM, marco tettamanti wrote: Hi John and Donna, I tried both of your methods, but unfortunately none solved my problem... I have tried to rename the file .fonts.conf, alone and, following the thread between Roland and you, together with .fonts.cache-1 and .fontconfig/ I also tried running Donna's script sh ./caret_prefs_stripper.sh. Helas, my entire X session always crashes when I import an Analyze image file. My problem seem to be different form Roland's and Veronica's ones, in that the problem is not "limited" to Caret, but it affects the entire X environment. Best, Marco John Harwell wrote: Marco, Another user had a problem similar to this. I believe it has to do with the FreeType library which gets used to create text characters that are drawn on the volume slices to show the voxel and its stereotaxic coordinate. See if there is a file in your home directory named ".fonts.conf" (note that the file begins with a period so use the command "ls -a" to see the file). If ".fonts.conf" exists, rename it, start Caret, and see if you can import a volume. For more info: http://www.mail-archive.com/caret-users@brainvis.wustl.edu/msg00892.html -- John Harwell [EMAIL PROTECTED] 314-362-3467 Department of Anatomy and Neurobiology Washington University School of Medicine 660 S. Euclid Ave.Box 8108 St. Louis, MO 63110 USA On Nov 29, 2006, at 10:42 AM, marco tettamanti wrote: Hi Donna and Hohn, I am experiencing a severe problem with my caret installation in linux: whenever I try to import an Analyze Volume file, my entire X session immediately crashes, including all applications and I have to login in KDE from scratch. I couldn't tell whether the problem is limited to the Import function only, because the system crashes so badly that I thought it would be better to obtain some feedback from you before doing some debugging. But all the other display functions of caret that I have tried out (rendering surfaces, overlaying metric maps and so on) seem to work fine. I first encountered the problem a few days ago. I completely ignore what could be the origin of the problem. I had used the same installation without any problems before, including the Import function. I have also tried to do a fresh install, of both versions 5.4 and 5.5, but the problem persists. I did some updates of KDE and xorg recently, though, and I suspect that the problem may have arosen since then. All other applications run fine, though. Also, I have installed the same .zip caret tar ball on another machine and there it runs fine... This is the kernel of my machine: Linux bll4 2.6.11-kanotix-11 #1 Sun May 29 22:32:10 CEST 2005 i686 GNU/Linux Any help would be greatly appreciated! Best, Marco --Marco Tettamanti, Ph.D. San Raffaele Scientific Institute Facoltà di Psicologia Via Olgettina 58 I-20132 Milano, Italy Tel. ++39-02-26434888 Fax ++39-02-26434892 Email: [EMAIL PROTECTED] ___ caret-users mailing list caret-users@brainvis.wustl.edu http://pulvinar.wustl.edu/mailman/listinfo/caret-users ___ caret-users mailing list caret-users@brainvis.wustl.edu http://pulvinar.wustl.edu/mailman/listinfo/caret-users -- Marco Tettamanti, Ph.D. San Raffaele Scientific Institute Facoltà di Psicologia Via Olgettina 58 I-20132 Milano, Italy Tel. ++39-02-26434888 Fax ++39-02-26434892 Email: [EMAIL PROTECTED]
Re: [caret-users] crash of X KDE session
Note to caret-users: St. Louis had a major winter storm last night, and I'm not sure who is in the office today, if anyone. I'm at home with power, but many people are without power. David is at UCDavis. Hi Marco, Okay, so display problem -- not I/O. You can try running gdb caret5, but if the crash is completely logging you out, your gdb session will exit, too. You've tried both Caret 5.4 and the latest Caret. It might be worth trying 5.3 if you can find a zip file for it on http://brainvis.wustl.edu/pub/caret (login pub, password download). Have you tried GNOME or another window system? I wonder if it's still something font related. Roland tried playing around with a lot of environment files, and he thought .fonts-conf was the one that did the trick, but he didn't seem absolutely sure about it. I wish I knew the answer, but like you, I'm still searching. > Hi Donna, > I have tried to use File: Open Volume Anatomy and Open Volume Functional on: > image.hdr > image.HEAD > image.nii > > as you suggested, but unfortunately they all cause the X session to crash. > > Thank you for you help! > Best, > Marco > > Donna Dierker wrote: >> Marco, >> Does the problem occur when you use File: Open Volume Anatomy (or functional) File to open the same file? >> If so, does it occur if you convert the file to NIfTI and/or AFNI? I'm guessing it will (e.g., suggesting a display issue, rather than a file I/O issue), but it helps to be sure. If you have trouble converting to another file format, then upload the file here, and I'll provide you the >> converted version: >> http://pulvinar.wustl.edu/cgi-bin/upload.cgi >> On 11/30/2006 04:08 AM, marco tettamanti wrote: >>> Hi John and Donna, >>> I tried both of your methods, but unfortunately none solved my problem... >>> I have tried to rename the file .fonts.conf, alone and, following the thread between Roland and you, together with .fonts.cache-1 and .fontconfig/ >>> I also tried running Donna's script sh ./caret_prefs_stripper.sh. Helas, my entire X session always crashes when I import an Analyze image file. >>> My problem seem to be different form Roland's and Veronica's ones, in that the problem is not "limited" to Caret, but it affects the entire X environment. >>> Best, >>> Marco >>> John Harwell wrote: Marco, Another user had a problem similar to this. I believe it has to do with the FreeType library which gets used to create text characters that are drawn on the volume slices to show the voxel and its stereotaxic coordinate. See if there is a file in your home directory named ".fonts.conf" (note that the file begins with a period so use the command "ls -a" to see the file). If ".fonts.conf" exists, rename it, start Caret, and see if you can import a volume. For more info: http://www.mail-archive.com/caret-users@brainvis.wustl.edu/msg00892.html -- John Harwell [EMAIL PROTECTED] 314-362-3467 Department of Anatomy and Neurobiology Washington University School of Medicine 660 S. Euclid Ave.Box 8108 St. Louis, MO 63110 USA On Nov 29, 2006, at 10:42 AM, marco tettamanti wrote: > Hi Donna and Hohn, > I am experiencing a severe problem with my caret installation in linux: whenever I try to import an Analyze Volume file, my entire X session immediately crashes, including all applications and I have to login in KDE from scratch. > I couldn't tell whether the problem is limited to the Import function only, because the system crashes so badly that I thought it would be better to obtain some feedback from you before doing some debugging. But all the other display functions of caret that I have tried out (rendering surfaces, overlaying metric maps and so on) seem to work fine. > I first encountered the problem a few days ago. I completely ignore what could be the origin of the problem. I had used the same installation without any problems before, including the Import function. I have also tried to do a fresh install, of both versions 5.4 and 5.5, but the problem persists. > I did some updates of KDE and xorg recently, though, and I suspect that the problem may have arosen since then. All other applications run fine, though. > Also, I have installed the same .zip caret tar ball on another machine and there it runs fine... > This is the kernel of my machine: > Linux bll4 2.6.11-kanotix-11 #1 Sun May 29 22:32:10 CEST 2005 i686 GNU/Linux > Any help would be greatly appreciated! > Best, > Marco > --Marco Tettamanti, Ph.D. > San Raffaele Scientific Institute > Facoltà di Psicologia > Via Olgettina 58 > I-20132 Milano, Italy > Tel. ++39-02-26434888 > Fax ++39-02-26434892 > Email: [EMAIL PROTECTED] > ___ > caret-users mailing list > caret-users@brainvis.wustl.edu > http://pulvinar.wustl.edu/mailman/listinfo/caret-users
Re: [caret-users] crash of X KDE session
Hi Marco, We had a problem similar to this that had to do with the "freetype" library that is used to render the stereotaxic coordinates on the volume display window. I have built a new version of Caret5 for linux that has an option, "-notext", that will prevent Caret5 from trying to draw any text characters. * Go to "http://brainmap.wustl.edu/pub/john/marco/";. Use the username "pub" and the password "download" to access the website. * Download the file caret5_exe_linux_debug.zip. This is a big file since it contains debugging information. If it takes too long to download, download caret5_exe_linux.zip instead. * Unzip this file which will produce the "caret5" executable. In the directory where you place the caret5 executable, start it with the command "./caret5 -notext". Load a volume into Caret and see if Caret crashes. If Caret does not crash after loading a volume, it probably means there is a problem with the freetype library on your computer (perhaps google freetype server crash. * If Caret still crashes with the "-notext" option and you downloaded the "debug" zip file do the following: Run the command "gdb ./ caret5". After about 15-30 seconds there will be a gdb prompt and enter the command "run". Load a volume into Caret. When Caret crashes enter the command "where" at the gdb and send me the output. If your X session crashes, log back in, and, in the same directory, see if there is a file named "core". If there is a file named core, enter the command "gdb ./caret5 core". At the gdb prompt, enter the command "where" and send me the output. Good Luck. -- John Harwell [EMAIL PROTECTED] 314-362-3467 Department of Anatomy and Neurobiology Washington University School of Medicine 660 S. Euclid Ave.Box 8108 St. Louis, MO 63110 USA On Dec 1, 2006, at 8:42 AM, marco tettamanti wrote: Hi Donna, I have tried to use File: Open Volume Anatomy and Open Volume Functional on: image.hdr image.HEAD image.nii as you suggested, but unfortunately they all cause the X session to crash. Thank you for you help! Best, Marco Donna Dierker wrote: Marco, Does the problem occur when you use File: Open Volume Anatomy (or functional) File to open the same file? If so, does it occur if you convert the file to NIfTI and/or AFNI? I'm guessing it will (e.g., suggesting a display issue, rather than a file I/O issue), but it helps to be sure. If you have trouble converting to another file format, then upload the file here, and I'll provide you the converted version: http://pulvinar.wustl.edu/cgi-bin/upload.cgi On 11/30/2006 04:08 AM, marco tettamanti wrote: Hi John and Donna, I tried both of your methods, but unfortunately none solved my problem... I have tried to rename the file .fonts.conf, alone and, following the thread between Roland and you, together with .fonts.cache-1 and .fontconfig/ I also tried running Donna's script sh ./caret_prefs_stripper.sh. Helas, my entire X session always crashes when I import an Analyze image file. My problem seem to be different form Roland's and Veronica's ones, in that the problem is not "limited" to Caret, but it affects the entire X environment. Best, Marco John Harwell wrote: Marco, Another user had a problem similar to this. I believe it has to do with the FreeType library which gets used to create text characters that are drawn on the volume slices to show the voxel and its stereotaxic coordinate. See if there is a file in your home directory named ".fonts.conf" (note that the file begins with a period so use the command "ls -a" to see the file). If ".fonts.conf" exists, rename it, start Caret, and see if you can import a volume. For more info: http://www.mail-archive.com/caret- [EMAIL PROTECTED]/msg00892.html -- John Harwell [EMAIL PROTECTED] 314-362-3467 Department of Anatomy and Neurobiology Washington University School of Medicine 660 S. Euclid Ave.Box 8108 St. Louis, MO 63110 USA On Nov 29, 2006, at 10:42 AM, marco tettamanti wrote: Hi Donna and Hohn, I am experiencing a severe problem with my caret installation in linux: whenever I try to import an Analyze Volume file, my entire X session immediately crashes, including all applications and I have to login in KDE from scratch. I couldn't tell whether the problem is limited to the Import function only, because the system crashes so badly that I thought it would be better to obtain some feedback from you before doing some debugging. But all the other display functions of caret that I have tried out (rendering surfaces, overlaying metric maps and so on) seem to work fine. I first encountered the problem a few days ago. I completely ignore what could be the origin of the problem. I had used the same installation without any problems before, including the I
