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.
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 < vinke@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 < 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 notfound'. 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/** SetupConfigurationhttps://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 myinstallation 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 bertorig.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 theperson 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/**compliancelinehttp://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.
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 <vinke@nmr.mgh.harvard.edu mailto:vinke@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 <vinke@nmr.mgh.harvard.edu <mailto: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 <mailto: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 <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
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 zkaufman@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 <vinke@nmr.mgh.harvard.edu mailto:vinke@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.txtSetUpFreeSurfer.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 <mailto: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 <mailto: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 <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-allhelp
-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@nmr.mgh.harvard.edu
-
clelia pellicano -
Louis Nicholas Vinke -
Z K