External Email - Use Caution
Hi Rachel,
Have you sourced Freesurfer install directory?
Here is help page on how to setup your Freesurfer environment on Linux -
https://secure-web.cisco.com/1Ub7K0QLalONiy0rW3bBM14kqwMElWC9S8wklOMGTNEoROLtbi5l-vQB0xjZDlZmXEwIz_EwWsnjfnVZZ7ljJGZLQ9
!
Rachel
*From: *Wighton, Paul <mailto:pwigh...@mgh.harvard.edu>
*Sent: *June 28, 2022 4:36 PM
*To: *freesurfer@nmr.mgh.harvard.edu
<mailto:Freesurfer@nmr.mgh.harvard.edu>
*Subject: *Re: [Freesurfer] Command Not Found
You don't often get email from pwigh...@mgh.harva
PM
*To: *freesurfer@nmr.mgh.harvard.edu
<mailto:Freesurfer@nmr.mgh.harvard.edu>
*Subject: *Re: [Freesurfer] Command Not Found
You don't often get email from pwigh...@mgh.harvard.edu. Learn why
this is important
<https://
rd.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Command Not Found
You don't often get email from pwigh...@mgh.harvard.edu. Learn why this is
important<https://
Hi Rachel,
Are you trying to run tkregister2? Looks like you forgot the t at the start of
the command.
-Paul
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Rachel Wagner
Sent: Tuesday, June 28, 2022 4:29 PM
To: freesurfer@nmr.mgh.harvard.edu
Subj
You can also use tkmeditfv and tksurferfv. They take the
tkmedit/tksurfer arguments but run freeview
On 5/13/2020 11:48 AM, Bruce Fischl wrote:
Hi Bo
tkmedit and tksurfer have been deprecated for years. Try using
freeview instead.
cheers
Bruce
On Wed, 13 May 2020, ZhangBo wrote:
Hi Bo
tkmedit and tksurfer have been deprecated for years. Try using freeview
instead.
cheers
Bruce
On Wed, 13 May 2020, ZhangBo wrote:
External Email - Use Caution
Hi teams,
After installing freesurfer-7.0.0 in MacOS 10.15.4, I followed the testing
guid in https://surfer.
External Email - Use Caution
Hello Samer,
The git bash shell on Windows will not be sufficient to run
freesurfer programs on Windows. Freesurfer is supported on CentOs Linux,
Ubuntu Linux and MacOS. However, some folks use the Ubuntu
shell as supported on Windows 10. This
Hi Laura,
So the 'freesurfer' command works but all other other freesurfer
commands (e.g. tkmedit, freeview) return "Command not found."?
Can you please provide me with the out of the 'echo $PATH' command? Thanks.
-Zeke
On 10/21/2013 12:34 PM, Laura Taylor wrote:
> Hi,
>
> I have just download
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
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 ima
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
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 f
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 freesur
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 worke
Christian,
I think the paths are still not correct. Try using
/home/user/Desktop
instead of
home/user/Desktop...
Also in 3) the variable of the subject directory is called SUBJECTS_DIR
instead of SUBJECTS so the command should be:
setenv SUBJECTS_DIR /home/user/Desktop/freesurfer/subjec
Ongoing Problems:
Bit of a delay having been away. Here is what I'm doing step by step and
then the error message at the bottom. Again I am using CentOS5 Linux shell
on a windows machine using Freesurfer V4.1.0 with the monitor settings on
32bit, and license file has been set up. Decided to try au
After you run the 'source $FREESURFER_HOME/SetUpFreeSurfer.csh' command,
is /home/user/Desktop/freesurfer in your 'path' environment variable?
On Wed, 2008-11-19 at 11:25 +, Christian Lambert wrote:
> I have explicitly set it like Nick suggested and ensured I have also
> sourced FreeSurferEn
I have explicitly set it like Nick suggested and ensured I have also sourced
FreeSurferEnv.csh. Same result unfortunately.
On Tue, Nov 18, 2008 at 5:08 PM, Nick Schmansky
<[EMAIL PROTECTED]>wrote:
> Christian,
>
> You may want to try explicitly setting your freesurfer home prior to
> sourcing, li
Christian,
You may want to try explicitly setting your freesurfer home prior to
sourcing, like this:
setenv FREESURFER_HOME /home/user/Desktop/freesurfer
source $FREESURFER_HOME/SetUpFreeSurfer.csh
i noticed in your output it has the path as 'Desktop/freesurfer', which
is not a full path, and pr
did you source $FREESURFER_HOME/FreeSurferEnv.csh?
On Tue, 18 Nov 2008,
Christian Lambert wrote:
I'm just starting out with freesurfer. I am using CentOS5 Linux shell on a
windows machine using Freesurfer V4.1.0 with the monitor settings on 32bit.
I have set up the license file and also config
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