Hi Saurabh,

On Feb 4, 2014, at 16:18 , Saurabh Thakur <srbhthkr@gmail.com> wrote:

> Hi Sebastian,
>
> I have copied in same tktools and tried to run the tkmedit2 subject1 rawavg.mgz
>
> got the output:
>
> saurabh@saurabh-Dell-System-XPS-L502X:/usr/local/freesurfer/tktools$ tkmedit2 subject1 rawavg.mgz
> bash: /usr/local/freesurfer/tktools/tkmedit2: Permission denied
> saurabh@saurabh-Dell-System-XPS-L502X:/usr/local/freesurfer/tktools$ sudo tkmedit2 subject1 rawavg.mgz
> sudo: tkmedit2: command not found
> saurabh@saurabh-Dell-System-XPS-L502X:/usr/local/freesurfer/tktools$
>

> Am i doing it right…?

        Oh, I guess tkmedit2 is not executable, so please run (from a shell in the directory where tkmedit2 is located):
chmod u+x tkmedit2
 and try to run it again from the directory where it is located:
"./tkmedit2 subject1 rawavg.mgz"

best regards
        Sebastian


>
>
> cheers
> Saurabh Thakur,
>
>
>
>
>
>
> On Tue, Feb 4, 2014 at 8:28 PM, Sebastian Moeller <sebastian.moeller1@rwth-aachen.de> wrote:
> Hi,
>
>
> On Feb 4, 2014, at 15:38 , Saurabh Thakur <srbhthkr@gmail.com> wrote:
>
> >
> > On Tue, Feb 4, 2014 at 7:41 PM, Sebastian Moeller <sebastian.moeller1@rwth-aachen.de> wrote:
> > tkmedit subject1 rawavg.mgz
> >
> > Hi Sebastian,
> >
> > tkmedit is properly get attached.
> > tat means tcsh is working properly.
> > //==========================================================//
> > saurabh@saurabh-Dell-System-XPS-L502X:/usr/local/freesurfer$ cd $SUBJECTS_DIR
> > saurabh@saurabh-Dell-System-XPS-L502X:~/Desktop/saurabh_freesurfer$
> >
> > saurabh@saurabh-Dell-System-XPS-L502X:/usr/local/freesurfer$ cat `which tkmedit`
> > #!/bin/tcsh -ef
> > source $FREESURFER_HOME/bin/tcl_setup
> > exec $FREESURFER_HOME/tktools/tkmedit.bin $argv
> > saurabh@saurabh-Dell-System-XPS-L502X:/usr/local/freesurfer$
> >
> >
> > saurabh@saurabh-Dell-System-XPS-L502X:/usr/local/freesurfer$ tkmedit subject1 rawavg.mgz
> > /usr/local/freesurfer/tktools/tkmedit.bin: Command not found.
> > saurabh@saurabh-Dell-System-XPS-L502X:/usr/local/freesurfer$
> > //===============================================================//
> >
> >
> > Still error is present…?
>
> Looks like it, so let me propose:
> 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
>         So in other words, open your preferred editor (edit?) create a new file with the name tkmedit2 in your home directory, and copy and paste the following into it and save it again:
>
>
> #!/bin/tcsh -Fe
> source $FREESURFER_HOME/bin/tcl_setup
> echo ${PATH}
> exec $FREESURFER_HOME/tktools/tkmedit.bin $argv
> exit 0
> #last line…
>
>
>
> and test:
> tkmedit2 subject1 rawavg.mgz
> (and post the output) in my last mail there was a typo here, the goal is to call the just created tkmedit2 and see whether the $PATCH contains the tktools directory.
>
> best regards
>         Sebastian
>
>
>
>
> >
> >
> > cheers
> > Saurabh Thakur,
> >
> >
> >
> >
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> >
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