Re: [Freesurfer] Re: mk-fieldsign problems
Can you run paint-sess with the -debug option and send us the output?
On Fri, Jan 06, 2006 at 03:36:50PM +, Jane Aspell wrote:
hi again
we've been trying various things to get mk-fieldsign to work: installing the
development version of freesurfer and trying it on a different computer, but
we
get the same error message. We thought that perhaps mk-fieldsign doesn't have
the same access permissions as the other tcl scripts or that it's not actually
looking in the same directory as for, e.g. tksurfer.tcl for which it gives the
full path:
surfer: using interface /home/jaspell/freesurfer/lib/tcl/tksurfer.tcl
Read /home/jaspell/freesurfer/surface_labels.txt, found 95 structures
tksurfer: run tcl script: mk-fieldsign.tcl
we are still stuck so would be really grateful for any tips!
thanks very much,
Jane
In message [EMAIL PROTECTED] Bruce
Fischl [EMAIL PROTECTED] writes:
hmmm, do you have it? If not, I've attached a copy.
cheers,
Bruc
e
On Tue, 3 Jan 2006, Jane Aspell wrote:
Hi
I would be really grateful if someone could help me with the problems I am
having with mk-fieldsign. Even after installing a new version of
freesurfer and
making various changes to libraries etc. when i run:
paint-sess -sf sessid -a rtopy -hemi rh i get the error below:
tksurfer: run tcl script: mk-fieldsign.tcl
couldn't read file mk-fieldsign.tcl: no such file or directory
even though mk-fieldsign.tcl is in the same directory as tksurfer.tcl
(which
works fine).
i am running Red Hat Linux release 9 (Shrike) and installed from
freesurfer-Linux-rh9-v2.2.tar.gz
any idea what to do?
thanks again for your help!
Jane
In message [EMAIL PROTECTED] Nick
Schmansky [EMAIL PROTECTED] writes:
Jane,
Concerning the libraries libitk3.2.so and libitcl3.2.so, Freesurfer does
not use these libraries any more (I think the older -20040218 release
did, however).
Do you have the environment variable ITCL_LIBRARY defined in your
startup .cshrc file? You can test if it is set by typing (in csh or
tcsh):
env|grep ITCL
If it is set (which it might be, from your older freesurfer
installation), then it should be deleted or commented-out from
your .cshrc (or possibly it was placed in your
$FREESURFER_HOME/SetUpFreeSurfer.csh file).
You can also just type this:
unsetenv ITCL_LIBRARY
and then try tkmedit.
If this is not the problem, can you tell me which OS you are running?
Type:
cat /etc/redhat-release
and
uname -a
A last ditch effort is to install the itcl libs, from this site:
http://rpmfind.net/linux/rpm2html/search.php?query=itcl
But this should not be necessary, as tkmedit that you have does not use
this library (I am truly puzzled why 'ldd' shows that it needs these
libs).
Thanks,
Nick
On Mon, 2005-12-12 at 11:40 +, Jane Aspell wrote:
hi nick
when i type ldd `which tkmedit` i get the ouput pasted below this
email.
libitk3.2.so and libitcl3.2.so are not found - could be the problem?
uncommenting 'source ${FSL_DIR}/etc/fslconf/fsl.csh' in
FreeSurferEnv.csh
(and typing 'unsetenv TCLLIBPATH') had no effect.
an earlier version of freesurfer(freesurfer-20040218) didn't give me
any of
these problems and tkmedit etc worked fine.
also, does ANYONE know how to interpret the colour coding (for
fovea/vertical
meridian etc) produced by the FsFast retinotopy analysis?!
thanks again!
jane
ldd `which tkmedit`
libtix8.1.8.3.so =
/home/jaspell/freesurfer/lib/tcltktixblt/lib/libtix8.1.8.3.so
(0x40017000)
libtk8.4.so =
/home/jaspell/freesurfer/lib/tcltktixblt/lib/libtk8.4.so
(0x40051000)
libtcl8.4.so =
/home/jaspell/freesurfer/lib/tcltktixblt/lib/libtcl8.4.so (0x40111000)
libglut.so.3 = /usr/lib/libglut.so.3 (0x401ba000)
libSM.so.6 = /usr/X11R6/lib/libSM.so.6 (0x401ef000)
libICE.so.6 = /usr/X11R6/lib/libICE.so.6 (0x401f8000)
libXmu.so.6 = /usr/X11R6/lib/libXmu.so.6 (0x4021)
libXi.so.6 = /usr/X11R6/lib/libXi.so.6 (0x40226000)
libGLU.so.1 = /usr/X11R6/lib/libGLU.so.1 (0x4022e000)
libGL.so.1 = /usr/X11R6/lib/libGL.so.1 (0x402ab000)
libX11.so.6 = /usr/X11R6/lib/libX11.so.6 (0x402ef000)
libjpeg.so.62 = /usr/lib/libjpeg.so.62 (0x403ce000)
libtiff.so.3 = /usr/lib/libtiff.so.3 (0x403ed000)
libcrypt.so.1 = /lib/libcrypt.so.1 (0x4042e000)
libz.so.1 = /usr/lib/libz.so.1 (0x4045b000)
libm.so.6 = /lib/tls/libm.so.6 (0x40469000)
libpthread.so.0 = /lib/tls/libpthread.so.0 (0x4048b000)
libc.so.6 = /lib/tls/libc.so.6 (0x4200)
libitk3.2.so = not found
libitcl3.2.so = not found
libdl.so.2 = /lib/libdl.so.2
Re: [Freesurfer] Re: mk-fieldsign problems
hmmm, do you have it? If not, I've attached a copy.
cheers,
Bruc
e
On Tue, 3 Jan 2006, Jane Aspell wrote:
Hi
I would be really grateful if someone could help me with the problems I am
having with mk-fieldsign. Even after installing a new version of freesurfer and
making various changes to libraries etc. when i run:
paint-sess -sf sessid -a rtopy -hemi rh i get the error below:
tksurfer: run tcl script: mk-fieldsign.tcl
couldn't read file mk-fieldsign.tcl: no such file or directory
even though mk-fieldsign.tcl is in the same directory as tksurfer.tcl (which
works fine).
i am running Red Hat Linux release 9 (Shrike) and installed from
freesurfer-Linux-rh9-v2.2.tar.gz
any idea what to do?
thanks again for your help!
Jane
In message [EMAIL PROTECTED] Nick
Schmansky [EMAIL PROTECTED] writes:
Jane,
Concerning the libraries libitk3.2.so and libitcl3.2.so, Freesurfer does
not use these libraries any more (I think the older -20040218 release
did, however).
Do you have the environment variable ITCL_LIBRARY defined in your
startup .cshrc file? You can test if it is set by typing (in csh or
tcsh):
env|grep ITCL
If it is set (which it might be, from your older freesurfer
installation), then it should be deleted or commented-out from
your .cshrc (or possibly it was placed in your
$FREESURFER_HOME/SetUpFreeSurfer.csh file).
You can also just type this:
unsetenv ITCL_LIBRARY
and then try tkmedit.
If this is not the problem, can you tell me which OS you are running?
Type:
cat /etc/redhat-release
and
uname -a
A last ditch effort is to install the itcl libs, from this site:
http://rpmfind.net/linux/rpm2html/search.php?query=itcl
But this should not be necessary, as tkmedit that you have does not use
this library (I am truly puzzled why 'ldd' shows that it needs these
libs).
Thanks,
Nick
On Mon, 2005-12-12 at 11:40 +, Jane Aspell wrote:
hi nick
when i type ldd `which tkmedit` i get the ouput pasted below this email.
libitk3.2.so and libitcl3.2.so are not found - could be the problem?
uncommenting 'source ${FSL_DIR}/etc/fslconf/fsl.csh' in FreeSurferEnv.csh
(and typing 'unsetenv TCLLIBPATH') had no effect.
an earlier version of freesurfer(freesurfer-20040218) didn't give me any of
these problems and tkmedit etc worked fine.
also, does ANYONE know how to interpret the colour coding (for fovea/vertical
meridian etc) produced by the FsFast retinotopy analysis?!
thanks again!
jane
ldd `which tkmedit`
libtix8.1.8.3.so =
/home/jaspell/freesurfer/lib/tcltktixblt/lib/libtix8.1.8.3.so (0x40017000)
libtk8.4.so = /home/jaspell/freesurfer/lib/tcltktixblt/lib/libtk8.4.so
(0x40051000)
libtcl8.4.so =
/home/jaspell/freesurfer/lib/tcltktixblt/lib/libtcl8.4.so (0x40111000)
libglut.so.3 = /usr/lib/libglut.so.3 (0x401ba000)
libSM.so.6 = /usr/X11R6/lib/libSM.so.6 (0x401ef000)
libICE.so.6 = /usr/X11R6/lib/libICE.so.6 (0x401f8000)
libXmu.so.6 = /usr/X11R6/lib/libXmu.so.6 (0x4021)
libXi.so.6 = /usr/X11R6/lib/libXi.so.6 (0x40226000)
libGLU.so.1 = /usr/X11R6/lib/libGLU.so.1 (0x4022e000)
libGL.so.1 = /usr/X11R6/lib/libGL.so.1 (0x402ab000)
libX11.so.6 = /usr/X11R6/lib/libX11.so.6 (0x402ef000)
libjpeg.so.62 = /usr/lib/libjpeg.so.62 (0x403ce000)
libtiff.so.3 = /usr/lib/libtiff.so.3 (0x403ed000)
libcrypt.so.1 = /lib/libcrypt.so.1 (0x4042e000)
libz.so.1 = /usr/lib/libz.so.1 (0x4045b000)
libm.so.6 = /lib/tls/libm.so.6 (0x40469000)
libpthread.so.0 = /lib/tls/libpthread.so.0 (0x4048b000)
libc.so.6 = /lib/tls/libc.so.6 (0x4200)
libitk3.2.so = not found
libitcl3.2.so = not found
libdl.so.2 = /lib/libdl.so.2 (0x4049a000)
libXt.so.6 = /usr/X11R6/lib/libXt.so.6 (0x4049e000)
libXext.so.6 = /usr/X11R6/lib/libXext.so.6 (0x404f)
libstdc++.so.5 = /usr/lib/libstdc++.so.5 (0x404ff000)
libgcc_s.so.1 = /lib/libgcc_s.so.1 (0x405b2000)
/lib/ld-linux.so.2 = /lib/ld-linux.so.2 (0x4000)
In message [EMAIL PROTECTED] Nick
Schmansky [EMAIL PROTECTED] writes:
Jane,
This is an unusual error, since tkmedit and tksurfer do not use the ITK
library. To figure out how libitk3.2.so is being referenced, can you
send me the output of this command:
ldd `which tkmedit`
I suspect there is some conflict between the FSL setup and Freesurfer,
as FSL does use ITK, and Freesurfer does not, but performs the FSL setup
(as a convenience to MGH-NMR users). Along this line, one option is to
edit the file FreeSurferEnv.csh (found in your $FREESURFER_HOME) and
comment-out this line:
source ${FSL_DIR}/etc/fslconf/fsl.csh
like this:
# source ${FSL_DIR}/etc/fslconf/fsl.csh
Another option is to type this after sourcing the freesurfer setup file:
unsetenv TCLLIBPATH
This last option is just a guess at a fix though.
Nick
On Mon, 2005-12-05 at 15:37 +, Jane Aspell wrote:
hi
i installed a newer version of freesurfer
Re: [Freesurfer] Re: mk-fieldsign problems
yes i already had the file. the one you sent me seemed to be a newer version
though, so i ran paint-sess using that, but it gives the same error message.
jane
In message [EMAIL PROTECTED] Bruce
Fischl [EMAIL PROTECTED] writes:
hmmm, do you have it? If not, I've attached a copy.
cheers,
Bruc
e
On Tue, 3 Jan 2006, Jane Aspell wrote:
Hi
I would be really grateful if someone could help me with the problems I am
having with mk-fieldsign. Even after installing a new version of freesurfer
and
making various changes to libraries etc. when i run:
paint-sess -sf sessid -a rtopy -hemi rh i get the error below:
tksurfer: run tcl script: mk-fieldsign.tcl
couldn't read file mk-fieldsign.tcl: no such file or directory
even though mk-fieldsign.tcl is in the same directory as tksurfer.tcl (which
works fine).
i am running Red Hat Linux release 9 (Shrike) and installed from
freesurfer-Linux-rh9-v2.2.tar.gz
any idea what to do?
thanks again for your help!
Jane
In message [EMAIL PROTECTED] Nick
Schmansky [EMAIL PROTECTED] writes:
Jane,
Concerning the libraries libitk3.2.so and libitcl3.2.so, Freesurfer does
not use these libraries any more (I think the older -20040218 release
did, however).
Do you have the environment variable ITCL_LIBRARY defined in your
startup .cshrc file? You can test if it is set by typing (in csh or
tcsh):
env|grep ITCL
If it is set (which it might be, from your older freesurfer
installation), then it should be deleted or commented-out from
your .cshrc (or possibly it was placed in your
$FREESURFER_HOME/SetUpFreeSurfer.csh file).
You can also just type this:
unsetenv ITCL_LIBRARY
and then try tkmedit.
If this is not the problem, can you tell me which OS you are running?
Type:
cat /etc/redhat-release
and
uname -a
A last ditch effort is to install the itcl libs, from this site:
http://rpmfind.net/linux/rpm2html/search.php?query=itcl
But this should not be necessary, as tkmedit that you have does not use
this library (I am truly puzzled why 'ldd' shows that it needs these
libs).
Thanks,
Nick
On Mon, 2005-12-12 at 11:40 +, Jane Aspell wrote:
hi nick
when i type ldd `which tkmedit` i get the ouput pasted below this email.
libitk3.2.so and libitcl3.2.so are not found - could be the problem?
uncommenting 'source ${FSL_DIR}/etc/fslconf/fsl.csh' in FreeSurferEnv.csh
(and typing 'unsetenv TCLLIBPATH') had no effect.
an earlier version of freesurfer(freesurfer-20040218) didn't give me any
of
these problems and tkmedit etc worked fine.
also, does ANYONE know how to interpret the colour coding (for
fovea/vertical
meridian etc) produced by the FsFast retinotopy analysis?!
thanks again!
jane
ldd `which tkmedit`
libtix8.1.8.3.so =
/home/jaspell/freesurfer/lib/tcltktixblt/lib/libtix8.1.8.3.so (0x40017000)
libtk8.4.so =
/home/jaspell/freesurfer/lib/tcltktixblt/lib/libtk8.4.so
(0x40051000)
libtcl8.4.so =
/home/jaspell/freesurfer/lib/tcltktixblt/lib/libtcl8.4.so (0x40111000)
libglut.so.3 = /usr/lib/libglut.so.3 (0x401ba000)
libSM.so.6 = /usr/X11R6/lib/libSM.so.6 (0x401ef000)
libICE.so.6 = /usr/X11R6/lib/libICE.so.6 (0x401f8000)
libXmu.so.6 = /usr/X11R6/lib/libXmu.so.6 (0x4021)
libXi.so.6 = /usr/X11R6/lib/libXi.so.6 (0x40226000)
libGLU.so.1 = /usr/X11R6/lib/libGLU.so.1 (0x4022e000)
libGL.so.1 = /usr/X11R6/lib/libGL.so.1 (0x402ab000)
libX11.so.6 = /usr/X11R6/lib/libX11.so.6 (0x402ef000)
libjpeg.so.62 = /usr/lib/libjpeg.so.62 (0x403ce000)
libtiff.so.3 = /usr/lib/libtiff.so.3 (0x403ed000)
libcrypt.so.1 = /lib/libcrypt.so.1 (0x4042e000)
libz.so.1 = /usr/lib/libz.so.1 (0x4045b000)
libm.so.6 = /lib/tls/libm.so.6 (0x40469000)
libpthread.so.0 = /lib/tls/libpthread.so.0 (0x4048b000)
libc.so.6 = /lib/tls/libc.so.6 (0x4200)
libitk3.2.so = not found
libitcl3.2.so = not found
libdl.so.2 = /lib/libdl.so.2 (0x4049a000)
libXt.so.6 = /usr/X11R6/lib/libXt.so.6 (0x4049e000)
libXext.so.6 = /usr/X11R6/lib/libXext.so.6 (0x404f)
libstdc++.so.5 = /usr/lib/libstdc++.so.5 (0x404ff000)
libgcc_s.so.1 = /lib/libgcc_s.so.1 (0x405b2000)
/lib/ld-linux.so.2 = /lib/ld-linux.so.2 (0x4000)
In message [EMAIL PROTECTED] Nick
Schmansky [EMAIL PROTECTED] writes:
Jane,
This is an unusual error, since tkmedit and tksurfer do not use the ITK
library. To figure out how libitk3.2.so is being referenced, can you
send me the output of this command:
ldd `which tkmedit`
I suspect there is some conflict between the FSL setup and Freesurfer,
as FSL does use ITK, and Freesurfer does not, but performs the FSL setup
(as a convenience to MGH-NMR users). Along this
