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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