Hi again,
On Feb 4, 2014, at 14:57 , Saurabh Thakur <srbht...@gmail.com> wrote:
>
> On Tue, Feb 4, 2014 at 7:15 PM, Sebastian Moeller
> <sebastian.moell...@rwth-aachen.de> wrote:
> tkmedit -f rawavg.mgz
>
>
> Hi Sebastian,
>
> //================================================================//
> saurabh@saurabh-Dell-System-XPS-L502X:~$ which tkmedit
> /usr/local/freesurfer/bin/tkmedit
> saurabh@saurabh-Dell-System-XPS-L502X:~$ which tkmedit.bin
> /usr/local/freesurfer/tktools/tkmedit.bin
> saurabh@saurabh-Dell-System-XPS-L502X:~$ echo $PATH
> /usr/local/freesurfer/bin:/usr/local/freesurfer/fsfast/bin:/usr/local/freesurfer/tktools:/usr/local/freesurfer/mni/bin:/usr/lib/lightdm/lightdm:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
> saurabh@saurabh-Dell-System-XPS-L502X:~$
Good, so the path is set up correctly (as expected otherwise the
freesurfer setup script would have complained)
>
>
>
>
> saurabh@saurabh-Dell-System-XPS-L502X:~$ cd $FREESURFER_HOME
Nah, cd ${SUBJECTS_DIR} not ${FREESURFER_HOME} we want a look at the
data directories, not the freesurfer distribution (but that does not matter
much see later).
> saurabh@saurabh-Dell-System-XPS-L502X:/usr/local/freesurfer$ cd subject1/mri
> bash: cd: subject1/mri: No such file or directory
> saurabh@saurabh-Dell-System-XPS-L502X:/usr/local/freesurfer$ ls -all
> total 392
> drwxr-xr-x 16 root root 4096 Feb 4 16:17 .
> drwxr-xr-x 12 root root 4096 Feb 4 15:48 ..
> -rw-r--r-- 1 root root 3302 Mar 1 2013 ASegStatsLUT.txt
> -rw-r--r-- 1 root root 728 Mar 1 2013 AUTHORS
> drwxr-xr-x 7 root root 4096 Mar 1 2013 average
> drwxr-xr-x 2 root root 36864 Mar 1 2013 bin
> -rw-r--r-- 1 root root 43 Mar 1 2013 build-stamp.txt
> drwxr-xr-x 3 root root 4096 Mar 1 2013 data
> -rw-r--r-- 1 root root 47514 Mar 1 2013 DefectLUT.txt
> drwxr-xr-x 3 root root 4096 Mar 1 2013 diffusion
> drwxr-xr-x 3 root root 4096 Mar 1 2013 docs
> -rw-r--r-- 1 root root 84833 Mar 1 2013 FreeSurferColorLUT.txt
> -rwxr-xr-x 1 root root 16760 Mar 1 2013 FreeSurferEnv.csh
> -rwxr-xr-x 1 root root 16846 Mar 1 2013 FreeSurferEnv.sh
> drwxr-xr-x 2 root root 4096 Mar 1 2013 fsafd
> drwxr-xr-x 5 root root 4096 Mar 1 2013 fsfast
> drwxr-xr-x 12 root root 4096 Mar 1 2013 lib
> -rw-r--r-- 1 root root 40 Feb 4 16:17 .license
> -rw-r--r-- 1 root root 39 Feb 4 15:51 .license~
> -rw-r--r-- 1 root root 10297 Mar 1 2013 LICENSE
> drwxr-xr-x 3 root root 4096 Mar 1 2013 matlab
> drwxr-xr-x 8 root root 4096 Feb 21 2010 mni
> -rw-r--r-- 1 root root 4793 Mar 1 2013 NOTICE
> -rw-r--r-- 1 root root 635 Mar 1 2013 README
> -rw-r--r-- 1 root root 28445 Mar 1 2013 SegmentNoLUT.txt
> drwxr-xr-x 2 root root 4096 Mar 1 2013 sessions
> -rwxr-xr-x 1 root root 1303 Mar 1 2013 SetUpFreeSurfer.csh
> -rwxr-xr-x 1 root root 1293 Mar 1 2013 SetUpFreeSurfer.sh
> -rw-r--r-- 1 root root 4104 Mar 1 2013 Simple_surface_labels2009.txt
> drwxr-xr-x 14 root root 4096 Mar 1 2013 subjects
> -rw-r--r-- 1 root root 1681 Mar 1 2013 tkmeditParcColorsCMA
> drwxr-xr-x 2 root root 4096 Mar 1 2013 tktools
> drwxr-xr-x 35 root root 4096 Mar 1 2013 trctrain
> -rw-r--r-- 1 root root 50 Mar 1 2013 VERSION
> -rw-r--r-- 1 root root 25944 Mar 1 2013 WMParcStatsLUT.txt
> saurabh@saurabh-Dell-System-XPS-L502X:/usr/local/freesurfer$ cd subject1/mri
> bash: cd: subject1/mri: No such file or directory
> saurabh@saurabh-Dell-System-XPS-L502X:/usr/local/freesurfer$ tkmedit -f
> rawavg.mgz
> /usr/local/freesurfer/tktools/tkmedit.bin: Command not found.
could you post the output of:
"cat `which tkmedit`"
Note the ` back ticks around the which tkmedit please?
Mine looks like:
hms-beagle:KOFIKO moeller$ cat `which tkmedit`
#!/bin/tcsh -ef
source $FREESURFER_HOME/bin/tcl_setup
exec $FREESURFER_HOME/tktools/tkmedit.bin $argv
hms-beagle:KOFIKO moeller$
I could imagine that somehow the invoked tcsh instance does not have the
correct path available. To test this hypothesis could you save the following to
your home directory as tkmedit2
#!/bin/tcsh -Fe
source $FREESURFER_HOME/bin/tcl_setup
echo ${PATH}
exec $FREESURFER_HOME/tktools/tkmedit.bin $argv
and test:
tkmedit subject1 rawavg.mgz
(and post the output)
best regards
Sebastian
> saurabh@saurabh-Dell-System-XPS-L502X:/usr/local/freesurfer$
>
> //===================================================================//
>
> I m working on laptop where as in other desktop in our lab its working fine.
>
> What should be the problem...?
>
> cheers
> Saurabh Thakur
>
>
>
>
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