Re: [Freesurfer] Command not found

: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Rachel Wagner Sent: Sunday, July 30, 2023 10:29 PM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Command not found External Email - Use Caution Hello all, I have not used freesurfer in a couple of months, and have returned to create

[Freesurfer] Command not found

External Email - Use Caution Hello all, I have not used freesurfer in a couple of months, and have returned to create a new cortical projection image. I’m having an issue with my commands, they don’t seem to be recognized anymore and I’m not sure why:

Re: [Freesurfer] Command Not Found

! 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.harvard.ed

Re: [Freesurfer] Command Not Found

: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.harvard.edu. Learn why this is important <https://secur

Re: [Freesurfer] Command Not Found

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://secur

Re: [Freesurfer] Command Not Found

Subject: [Freesurfer] Command Not Found External Email - Use Caution Hello, Thank you for your help! I am trying to register my spm image and am getting the following error: developer@developer-VirtualBox:~$ kregister2 --s home --mov updated.mgz --regheader --reg register.dat --surf

[Freesurfer] Command Not Found

External Email - Use Caution Hello, Thank you for your help! I am trying to register my spm image and am getting the following error: developer@developer-VirtualBox:~$ kregister2 --s home --mov updated.mgz --regheader --reg register.dat --surf orig kregister2: command not

Re: [Freesurfer] command not found: tksurfer

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:

Re: [Freesurfer] command not found: tksurfer

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 

[Freesurfer] command not found: tksurfer

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.nmr.mgh.harvard.edu/fswiki/TestingFreeSurfer. It is ok for freeview, however for tksurfer and tkmedit, I get errors "zsh: command not found:

Re: [Freesurfer] Command not found

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

[Freesurfer] Command not found

External Email - Use Caution Hello, I am having trouble adding Freesurfer onto my PC. I have the program downloaded, but when I attempt to input a command from the Freesurfer program, it tells me that my command was not found. [image: image.png] This is my first time downloading

[Freesurfer] command not found - unable to set up freesurfer

Hi, I have just downloaded and I thought installed freesurfer on a Debian system (Debian 3.2.51-1 x86_64 GNU/Linux). However when I go to test the install by typing in freeview (or any other command) in the terminal window I get the following: % freeview freeview: Command not found. Before

Re: [Freesurfer] command not found - unable to set up freesurfer

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 downloaded

Re: [Freesurfer] command not found

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

Re: [Freesurfer] command not found

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

Re: [Freesurfer] command not found

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

Re: [Freesurfer] command not found

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

[Freesurfer] command not found

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

Re: [Freesurfer] Command Not Found

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

Re: [Freesurfer] Command Not Found

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

[Freesurfer] Command Not Found

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 configured freesurfer as per the wiki pages: [EMAIL PROTECTED] ~]$ source

Re: [Freesurfer] Command Not Found

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

Re: [Freesurfer] Command Not Found

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