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 04:08 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]
_______________________________________________
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]
_______________________________________________
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]
