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
-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
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