Hi Sebastian ,Bruce and Markus.
I got the freesurfer running using
freesurfer-x86_64-unknown-linux-gnu-stable5-20130513
Thanks for all your help.
cheers Saurabh Thakur,
On Tue, Feb 4, 2014 at 9:18 PM, Sebastian Moeller < sebastian.moeller1@rwth-aachen.de> wrote:
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 ashell 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 anew 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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