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 vinke@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 <vinke@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 -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 . 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.