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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