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 <[email protected]> wrote: Hi Saurabh, On Feb 4, 2014, at 16:18 , Saurabh Thakur <[email protected]> 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 <[email protected]> wrote: > Hi, > > > On Feb 4, 2014, at 15:38 , Saurabh Thakur <[email protected]> wrote: > > > > > On Tue, Feb 4, 2014 at 7:41 PM, Sebastian Moeller <[email protected]> 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 > > [email protected] > > 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 > [email protected] > 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.
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