Hi, I have tried :
>> setenv FREESURFER_HOME /Applications/freesurfer >> source $FREESURFER_HOME/SetUpFreesurfer.csh >> tkmedit -f $FREESURFER_HOME/subjects/sample-001.mgz I got this message: dyld: Library not loaded: /opt/X11/lib/libGLU.1.dylib Referenced from: /Applications/freesurfer/bin/qdec.bin Reason: image not found Trace/BPT trap I checked online and found here how to do. It was a problem with XQuartz. https://surfer.nmr.mgh.harvard.edu/fswiki/freesurfer_GUIs_troubleshooting Now it is working. Thank you, Clelia On Fri, May 24, 2013 at 7:26 PM, Z K <zkauf...@nmr.mgh.harvard.edu> wrote: > 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 >
_______________________________________________ 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.
