Clelia, Please type the following commands in the terminal window and provide us any error message you may receive.
>> setenv FREESURFER_HOME /Applications/freesurfer >> source $FREESURFER_HOME/SetUpFreesurfer.csh >> tkmedit -f $FREESURFER_HOME/subjects/sample-001.mgz If a window with an image pops open than freesurfer is installed and ready to go. If not than please provide whatever error message you may receive. -Zeke On 05/24/2013 12:15 PM, clelia pellicano wrote: > 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 <mailto: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 <mailto: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 > <mailto: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. > > > > > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
