Hi Louise, yes, teh FreeSurfer related commands are still not found. The other thing is that I had problem with license file. I have created a file in Applications/Freesurfer named .license and tried to copy inside le license key but I'm not sure that it worked beacuse if I write cd .license I get 'it is not a file not a directory'. Thanks
Clelia On Fri, May 24, 2013 at 5:09 PM, Louis Nicholas Vinke < vi...@nmr.mgh.harvard.edu> wrote: > Hi Clelia, > That mv command is failing presumably because SetUpFreeSurfer.txt does not > exist in that directory. What are you trying to do with the mv command? > > It does look like freesurfer was sourced successfully. Are the FreeSurfer > related commands still not found? > > Don't forget to cc the freesurfer mailing list. > > -Louis > > On Fri, 24 May 2013, clelia pellicano wrote: > > Hi Louise, >> I'm now using tcsh. Here what I did >> >> [dyn1097-8:~] cpellica% setenv FREESURFER_HOME >> /Applications/freesurfer >> [dyn1097-8:~] cpellica% source /Applications/freesurfer/** >> SetUpFreesurfer.csh >> -------- freesurfer-Darwin-lion-stable-**pub-v5.3.0 -------- >> Setting up environment for FreeSurfer/FS-FAST (and FSL) >> FREESURFER_HOME /Applications/freesurfer >> FSFAST_HOME /Applications/freesurfer/**fsfast >> FSF_OUTPUT_FORMAT nii.gz >> SUBJECTS_DIR /Applications/freesurfer/**subjects >> MNI_DIR /Applications/freesurfer/mni >> FSL_DIR /usr/local/fsl >> [dyn1097-8:~] cpellica% mv SetUpFreeSurfer.txt SetUpFreeSurfer.csh >> mv: rename SetUpFreeSurfer.txt to SetUpFreeSurfer.csh: No such file or >> directory >> >> Do you have any advice? >> >> Thanks >> >> Clelia >> >> >> >> >> >> On Fri, May 24, 2013 at 3:04 PM, Louis Nicholas Vinke < >> vi...@nmr.mgh.harvard.edu> wrote: >> Hi Clelia, >> What do you run to source FS and do you get any output in your >> terminal after doing so? What operating system are >> you running? You might try using c-shell instead of bash. >> -Louis >> >> On Fri, 24 May 2013, clelia pellicano wrote: >> >> Hi Louis, >> thank you for your answer. >> I sourced freesurfer again, but I still get 'command not >> found'. >> What can I try? >> Thank you, >> >> Clelia >> >> >> On Thu, May 23, 2013 at 7:15 PM, Louis Nicholas Vinke < >> vi...@nmr.mgh.harvard.edu> wrote: >> Hi Clelia, >> If this is in a new terminal then you'll have to source >> freesurfer again. See here for details: >> https://surfer.nmr.mgh.**harvard.edu/fswiki/** >> SetupConfiguration<https://surfer.nmr.mgh.harvard.edu/fswiki/SetupConfiguration> >> -Louis >> >> On Wed, 22 May 2013, clelia pellicano wrote: >> >> Hi, >> I have run recon-all -s bert -all to try my >> installation and it worked. >> Now, when I try to use other command (and also >> again recon-all -s bert -all) I always get >> this: >> >> dyn1097-8:subjects cpellica$ tkmedit bert orig.mgz >> -bash: tkmedit: command not found >> dyn1097-8:subjects cpellica$ tkmedit -s bert >> orig.mgz >> -bash: tkmedit: command not found >> dyn1097-8:subjects cpellica$ tksurfer -s bert rh >> pial >> -bash: tksurfer: command not found >> dyn1097-8:subjects cpellica$ qdec >> -bash: qdec: command not found >> dyn1097-8:subjects cpellica$ recon-all help >> -bash: recon-all: command not found >> dyn1097-8:subjects cpellica$ recon-all -s bert >> -all >> -bash: recon-all: command not found >> >> >> I don't know how to do. Please, could you help me? >> >> Thanks >> >> Clelia >> >> >> >> >> 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<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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