Yes, delete tksurfer.new.tcl.
We stopped using tksurfer.new.tcl a while before that release and removed it from the distribution, but unfortunately, our upgrade script did not erase it. So you probably upgraded an old installation with the 2004 version, and it didn't remove the old tksurfer.new.tcl. tksurfer is hardcoded to first look for and use tksurfer.new.tcl, then tksurfer.tcl. This is for 'historical reasons'.
On Sat, 9 Jul 2005 xmeadow@uchicago.edu wrote:
Hi,
I just opened up freesurfer and did some stuff and I got the following in the logs:
surfer: using interface /opt/freesurfer_alpha/lib/tcl/tksurfer.new.tcl
The /opt/freesurfer_alpha is correct, but I'm not sure what the tksurfer.new.tcl is. Inside freesurfer_alpha/lib I've got a tcl and tcl.new directory. Iniside those folders I've got:
tcl.new/tksurfer.new.tcl tcl.new/tksurfer.tcl
tcl/tksurfer.new.tcl.020617 tcl/tksurfer.tcl.020318 tcl/tksurfer.tcl tcl/tksurfer.tcl.040219 tcl/tksurfer.new.tcl tcl/tksurfer.tcl.020107 tcl/tksurfer.tcl.120400
But I don't know which of these I should be using. Is there a way I can check which of these is the correct one? Also, in which preference file to I tell Freesurfer to look at the correct tksurfer.tcl file? Thanks very much.
Xander
---- Original message ----
Date: Fri, 8 Jul 2005 17:35:18 -0400 (EDT) From: Kevin Teich kteich@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Problem filling labels To: Xander Meadow xmeadow@uchicago.edu
Actually, I just veried that those are the correct versions
to be used
together.
The only other thing I can think of is that the binary is
finding a
different version of the script. When you run tksurfer, look
for a line of
output that looks like:
surfer: using interface .../tksurfer.tcl
and make sure the .../ part is $FREESURFER_HOME/lib/tcl. Then
make sure
that 'which tksurfer' is pointing to the same $FREESURFER_HOME installation.
On Fri, 8 Jul 2005, Xander Meadow wrote:
I'm not entirely sure where we got our current version
from. If the easiest
thing to do would be just e-mail me the new script then I
am definitely in
favor of that. I have other machines with freesurfer on
them, and it's
likely they all have this problem, would the easiest thing
to do, be to just
download a new fresh copy of freesurfer from the freesurfer
website? But,
please if it's not too much trouble, send me the new script
so I can install
that and start drawing. Thank you again so much for
helping me with this.
Xander
On Jul 8, 2005, at 3:39 PM, Kevin Teich wrote:
Yes, that version is from 2004, while the script file
you're using is from
- Did you get a new version from us at some point? If
so, you should've
gotten a corresponding tksurfer.tcl file. If not, I can
give you one.
On Fri, 8 Jul 2005, Xander Meadow wrote:
freesurfer_alpha/bin/tksurfer --all-info
ProgramName: tksurfer ProgramArguments: --all-info
ProgramVersion: $Name:
$ TimeStamp: 05/07/08-20:36:58-GMT CVS: $Id: tksurfer.c,v
1.61 2004/01/05
20:36:23 fischl Exp $ User: xmeadow Machine: andrew
Platform: Linux
PlatformVersion: 2.6.9-11.ELsmp CompilerName: GCC
CompilerVersion: 29600
Xander
On Jul 8, 2005, at 3:26 PM, Kevin Teich wrote:
Ah, I think the version of tksurfer you are using is
much newer than the
one that should be associated with the script. What do
you get if you
try: tksurfer --all-info On Sat, 9 Jul 2005 xmeadow@uchicago.edu wrote: > Hi, > It used to work in the past, but I don't know what
might have
> changed. The machines run uptodate each night to stay
current
> with Redhat patches, but I'm not sure what might have been > updated right before this stopped working. As for tksurfer > --version > freesurfer_alpha/bin/Linux/tksurfer --version > $ > I'm not sure what the means though, as it's not a
number, just
> the dollar sign. Does this give you any clues? Thanks so > much for helping me out with this. >> Xander > ---- Original message ---- >> Date: Fri, 8 Jul 2005 13:17:45 -0400 (EDT) >> From: Kevin Teich kteich@nmr.mgh.harvard.edu >> Subject: Re: [Freesurfer] Problem filling labels >> To: xmeadow@uchicago.edu >> I can't duplicate this at all. Has this ever worked
for you,
> or did it >> stop working? >> Can you give me the output of >> tksurfer --version >> On Fri, 8 Jul 2005 xmeadow@uchicago.edu wrote: >>> In the Fill box the one I am trying to use is "Up to and >>> including boundaries" by itself, but I've also tried
the other
>>> possible combinations in a hope that it would work.
Also,
>>> this error always happens regardless of whatever else
I've
> done. >>>> Xander >>> ---- Original message ---- >>>> Date: Thu, 7 Jul 2005 17:27:20 -0400 (EDT) >>>> From: Kevin Teich kteich@nmr.mgh.harvard.edu >>>> Subject: Re: [Freesurfer] Problem filling labels >>>> To: Xander Meadow xmeadow@uchicago.edu >>>> Cc: freesurfer@nmr.mgh.harvard.edu >>>> What were your settings in the Fill dialog box? Does
this
>>> always happen, >>>> or only with a specific combination of options? >>>> On Thu, 7 Jul 2005, Xander Meadow wrote: >>>>> Hi, >>>>> I was trying to make an ROI on an inflated surface. >>> Specifically I can >>>>> recreate the error if I: >>>>> Mark a bunch of vertices >>>>> Create fill boundary >>>>> clear all marked vertices >>>>> mark a vertex within the filled boundary >>>>> then try to fill it. >>>>> I did all this via the GUI. >>>>> Does this help? Is there anything else I can tell
you that
>>> might help? >>>>>> Xander >>>>> On Jul 7, 2005, at 3:43 PM, Kevin Teich wrote: >>>>>>> Here is the file you requested: >>>>>> Hm, that appears to be OK. What action were you
performing
>>> when you got the >>>>>> error? >>>>>>> Can you send me the file: >>>>>>> $FREESURFER_HOME/lib/tcl/tksurfer.tcl >>>>>>> On Thu, 7 Jul 2005 xmeadow@uchicago.edu wrote: >>>>>>>> Hi, >>>>>>>> I'm having trouble filling labels using
Freesurfer version
>>>>>>>> 0.9(33y). I'm running RedHat Enterprise WS v.4.
I looked
>>>>>>>> through the mail archives and found that this
problem has
>>>>>>>> happened in the past, the post is here: >
http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg00042.html
>>>>>>>> I get the same error: >>>>>>>> Error: Wrong # args: fill_flood_from_cursor >>>>>>>> dont_cross_boundary dont_cross_label dont_cross_cmid >>>>>>>> dont_cross_fthresh use_multiple_seeds action
argument
>>>>>>>> I have a .xdebug_tkmedit if it would help debug this > issue. >>>>>>>> Does anyone know what I can do to fix this?
Thank you
>>> very much. >>>>>> -- >>>>>> Kevin Teich >>>> -- >>>> Kevin Teich >> --
>> Kevin Teich
Kevin Teich
-- Kevin Teich
-- Kevin Teich