glad to hear it worked out Bruce On Wed, 5 Feb 2014, Saurabh Thakur wrote:
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 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,
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to
whom it is
addressed. If you believe this e-mail was sent to you in error and
the e-mail
contains patient information, please contact the Partners
Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to
you in error
but does not contain patient information, please contact the
sender and properly
dispose of the e-mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to
whom it is
addressed. If you believe this e-mail was sent to you in error and
the e-mail
contains patient information, please contact the Partners Compliance
HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to
you in error
but does not contain patient information, please contact the sender
and properly
dispose of the e-mail.