Re: [caret-users] crash of X KDE session
Hi John, I have tried unlimiting the coredumpsize from a tcsh shell (as I was indeed using a bash shell and the coredumpsize was limited to 0 kbytes) but, for some reasons, even if caret crashes no core file gets written out. All the display functions that I have tried out (rendering surfaces, overlaying metric maps and so on) seem to work fine. But I couldn't tell whether the problem is really limited to opening volumes, as I haven't tried out many other things. I will try to upgrade the graphic card drivers! Thanks! Marco John Harwell wrote: Marco, The creation of a core file may be inhibited. So, make sure you are running one of the c-shell variances (enter the command "/bin/csh" or "/bin/tcsh". Enter the command "limit". If "coredumpsize" is anything but unlimited, do the following: * Enter the command "unlimit coredumpsize". * Enter "limit" to verify that "coredumpsize" is unlimited. * Run caret by typing "./caret5" but do not use gdb. * Import the volume to get Caret to crash. * Relogin. * Enter the command "gdb ./caret5 core". * Type "where" at the gdb prompt and send me the output. Are your able to load a surface into Caret5? Have you tried updating your graphics card drivers? John On Dec 5, 2006, at 10:24 AM, marco tettamanti wrote: Hi John, I have downloaded caret5_exe_linux_debug and ran it, but strange things happened... :-| 1) First, I ran the debug executable as caret5 -notext as you suggested: I selected File Import, and, wow! caret opened the file. I did the same with File Open and it worked. Solved, I thought: must be the freetype library. So I clicked on the upper right corner to quit Caret and, whoops, the X session crashed. 2) Second, I started X again, and wanted to replicate this behavior. I launched the debug caret5 -notext, choose File Import... Well, this time the X session crashed at this point already. 3) Third, I followed your suggestion and typed gdb ./caret5 (the debug version), choose File Import and the X session crashed. Unfortunately, at rebooting there was no core file in the directory from where I launched caret. 4) I have tried to re-download caret5_exe_linux_debug to check whether something had gone corrupted during 1), but Caret continued to crash right after a File Import command. Thank you again! Marco John Harwell wrote: 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 04:0
Re: [caret-users] crash of X KDE session
Marco, The creation of a core file may be inhibited. So, make sure you are running one of the c-shell variances (enter the command "/bin/csh" or "/bin/tcsh". Enter the command "limit". If "coredumpsize" is anything but unlimited, do the following: * Enter the command "unlimit coredumpsize". * Enter "limit" to verify that "coredumpsize" is unlimited. * Run caret by typing "./caret5" but do not use gdb. * Import the volume to get Caret to crash. * Relogin. * Enter the command "gdb ./caret5 core". * Type "where" at the gdb prompt and send me the output. Are your able to load a surface into Caret5? Have you tried updating your graphics card drivers? John On Dec 5, 2006, at 10:24 AM, marco tettamanti wrote: Hi John, I have downloaded caret5_exe_linux_debug and ran it, but strange things happened... :-| 1) First, I ran the debug executable as caret5 -notext as you suggested: I selected File Import, and, wow! caret opened the file. I did the same with File Open and it worked. Solved, I thought: must be the freetype library. So I clicked on the upper right corner to quit Caret and, whoops, the X session crashed. 2) Second, I started X again, and wanted to replicate this behavior. I launched the debug caret5 -notext, choose File Import... Well, this time the X session crashed at this point already. 3) Third, I followed your suggestion and typed gdb ./caret5 (the debug version), choose File Import and the X session crashed. Unfortunately, at rebooting there was no core file in the directory from where I launched caret. 4) I have tried to re-download caret5_exe_linux_debug to check whether something had gone corrupted during 1), but Caret continued to crash right after a File Import command. Thank you again! Marco John Harwell wrote: 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 no
Re: [caret-users] crash of X KDE session
Hi John, I have downloaded caret5_exe_linux_debug and ran it, but strange things happened... :-| 1) First, I ran the debug executable as caret5 -notext as you suggested: I selected File Import, and, wow! caret opened the file. I did the same with File Open and it worked. Solved, I thought: must be the freetype library. So I clicked on the upper right corner to quit Caret and, whoops, the X session crashed. 2) Second, I started X again, and wanted to replicate this behavior. I launched the debug caret5 -notext, choose File Import... Well, this time the X session crashed at this point already. 3) Third, I followed your suggestion and typed gdb ./caret5 (the debug version), choose File Import and the X session crashed. Unfortunately, at rebooting there was no core file in the directory from where I launched caret. 4) I have tried to re-download caret5_exe_linux_debug to check whether something had gone corrupted during 1), but Caret continued to crash right after a File Import command. Thank you again! Marco John Harwell wrote: 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-users@brainvis.wustl.edu/msg00892.html -- John Harwell [EMAIL PROTECTE
Re: [caret-users] crash of X KDE session
Hi John and Donna,
thank you for your suggestions! I will no try to dowload the debug
release and follow your instructions.
In the meantime, I ran Caret with the 'strace' linux diagnostic command,
hoping it may help you to trace the problem. I have attached the file
with the whole text output.
I am a quite naive linux user, so I do not know how to read the output
of the trace command, but as some point toward the end of the file I
have found:
open("/mnt/hda5/work/negazione/neg_01b/anat3D/mean_anat3D.hdr",
O_RDONLY|O_LARGEFILE) = 12
and at the end of the text output:
write(7, "\221\5\4\0\17\0\300\3\16\0\300\3\1\0\0\0", 16) = 16
read(7, 0xbfffcbbc, 32) = -1 EAGAIN (Resource
temporarily unavailable)
poll([{fd=7, events=POLLIN, revents=POLLIN|POLLERR|POLLHUP}], 1, -1) = 1
read(7, 0xbfffcbbc, 32) = -1 ECONNRESET (Connection
reset by peer)
write(2, "caret5: Fatal IO error: client k"..., 38) = 38
munmap(0xb7723000, 163840) = 0
write(6, "@", 1)= 1
close(6)= 0
close(5)= 0
close(3)= 0
close(4)= 0
munmap(0xb7955000, 4096)= 0
exit_group(1) = ?
I will let you know about using debug_caret!
Best,
Marco
John Harwell wrote:
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 beg
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
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 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
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 -- Donna L. Dierker (Formerly Donna Hanlon; no change in marital status -- see http://home.att.net/~donna.hanlon for details.)
Re: [caret-users] crash of X KDE session
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
Hi Marco, Although your problem is a bit different, another possible culprit is the .caret5_preferences file: http://brainvis.wustl.edu/pipermail/caret-users/2006-November/000931.html We're still struggling with this problem at University of Washington. Today I asked Veronica to try the attached script, which strips the recent files and directories from the caret preferences before launching caret. I'm curious whether it helps in your case, in case the .fonts.conf trick fails. Let us know what you find. On 11/29/2006 11:19 AM, 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 -- Donna L. Dierker (Formerly Donna Hanlon; no change in marital status -- see http://home.att.net/~donna.hanlon for details.) caret_prefs_stripper.sh Description: Bourne shell script
Re: [caret-users] crash of X KDE session
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 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] crash of X KDE session
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]
