Hello,
I am installing Freesurfer with my limited coding knowledge and this problem with freeview came up when I was trying to view the volumes of recon-ed subject.
lab@lab-ThinkStation-E31:~/Desktop/freesurfer/subjects$ freeview -v practice/mri/T1/mgz No command 'freeview' found, did you mean: Command 'treeview' from package 'treeview' (multiverse) freeview: command not found
I checked and freeview is in the bin, and I even tried to install it according to its file by sourcing tcl_setup and others, but then this error comes up:
lab@lab-ThinkStation-E31:~/Desktop/freesurfer/bin$ source tcl_setup bash: tcl_setup: line 47: syntax error near unexpected token `setenv' bash: tcl_setup: line 47: ` if ( -e $TCLLIBPATH/tcl8.3 ) setenv TCL_LIBRARY $TCLLIBPATH/tcl8.3'
Can someone please give me any direction for how to solve this issue. I would appreciate the help very much. (Freesurfer version 6 & Ubuntu 16.04)
Thank you all, Idil
Hi Idil
how do you setup freesurfer? If you are using bash (and it looks like you are) you should source the *.sh file, not the *.csh. Also, note that you should use T1.mgz not T1/mgz in your freeview command line cheers Bruce On Tue, 11 Jul 2017, Yagmur Ozdemir 19 wrote:
Hello,
I am installing Freesurfer with my limited coding knowledge and this problem with freeview came up when I was trying to view the volumes of recon-ed subject.
lab@lab-ThinkStation-E31:~/Desktop/freesurfer/subjects$ freeview -v practice/mri/T1/mgz No command 'freeview' found, did you mean: Command 'treeview' from package 'treeview' (multiverse) freeview: command not found
I checked and freeview is in the bin, and I even tried to install it according to its file by sourcing tcl_setup and others, but then this error comes up:
lab@lab-ThinkStation-E31:~/Desktop/freesurfer/bin$ source tcl_setup bash: tcl_setup: line 47: syntax error near unexpected token `setenv' bash: tcl_setup: line 47: ` if ( -e $TCLLIBPATH/tcl8.3 ) setenv TCL_LIBRARY $TCLLIBPATH/tcl8.3'
Can someone please give me any direction for how to solve this issue. I would appreciate the help very much. (Freesurfer version 6 & Ubuntu 16.04)
Thank you all, Idil
Hello, I only followed the steps in the install/download page and installed tcsh because it was not running recon-all. Are you saying that I should set up freeview by sourcing those three files and use the *.csh extension? When opening the terminal again after recon-all to run this I did not do any additional set up. I also remember using .sh when following the steps on the install page. The system does not recognize freeview even when I just use the command alone. Sorry my knowledge pertaining to software use is pretty elementary and there is no one to ask.
Thank you for the help, Idil
________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Tuesday, July 11, 2017 6:03 PM To: Freesurfer support list Subject: Re: [Freesurfer] freeview command error
Hi Idil
how do you setup freesurfer? If you are using bash (and it looks like you are) you should source the *.sh file, not the *.csh. Also, note that you should use T1.mgz not T1/mgz in your freeview command line cheers Bruce On Tue, 11 Jul 2017, Yagmur Ozdemir 19 wrote:
Hello,
I am installing Freesurfer with my limited coding knowledge and this problem with freeview came up when I was trying to view the volumes of recon-ed subject.
lab@lab-ThinkStation-E31:~/Desktop/freesurfer/subjects$ freeview -v practice/mri/T1/mgz No command 'freeview' found, did you mean: Command 'treeview' from package 'treeview' (multiverse) freeview: command not found
I checked and freeview is in the bin, and I even tried to install it according to its file by sourcing tcl_setup and others, but then this error comes up:
lab@lab-ThinkStation-E31:~/Desktop/freesurfer/bin$ source tcl_setup bash: tcl_setup: line 47: syntax error near unexpected token `setenv' bash: tcl_setup: line 47: ` if ( -e $TCLLIBPATH/tcl8.3 ) setenv TCL_LIBRARY $TCLLIBPATH/tcl8.3'
Can someone please give me any direction for how to solve this issue. I would appreciate the help very much. (Freesurfer version 6 & Ubuntu 16.04)
Thank you all, Idil
Hi Idil
do you know what shell you are using in the terminal that you are trying to call freeview from? On Tue, 11 Jul 2017, Yagmur Ozdemir 19 wrote:
Hello, I only followed the steps in the install/download page and installed tcsh because it was not running recon-all. Are you saying that I should set up freeview by sourcing those three files and use the *.csh extension? When opening the terminal again after recon-all to run this I did not do any additional set up. I also remember using .sh when following the steps on the install page. The system does not recognize freeview even when I just use the command alone. Sorry my knowledge pertaining to software use is pretty elementary and there is no one to ask.
Thank you for the help, Idil
From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Tuesday, July 11, 2017 6:03 PM To: Freesurfer support list Subject: Re: [Freesurfer] freeview command error
Hi Idil
how do you setup freesurfer? If you are using bash (and it looks like you are) you should source the *.sh file, not the *.csh. Also, note that you should use T1.mgz not T1/mgz in your freeview command line cheers Bruce On Tue, 11 Jul 2017, Yagmur Ozdemir 19 wrote:
Hello,
I am installing Freesurfer with my limited coding knowledge and this problem with freeview came up when I was trying to view the volumes of recon-ed subject.
lab@lab-ThinkStation-E31:~/Desktop/freesurfer/subjects$ freeview -v practice/mri/T1/mgz No command 'freeview' found, did you mean: Command 'treeview' from package 'treeview' (multiverse) freeview: command not found
I checked and freeview is in the bin, and I even tried to install it according to its file by sourcing tcl_setup and others, but then this error comes up:
lab@lab-ThinkStation-E31:~/Desktop/freesurfer/bin$ source tcl_setup bash: tcl_setup: line 47: syntax error near unexpected token `setenv' bash: tcl_setup: line 47: ` if ( -e $TCLLIBPATH/tcl8.3 ) setenv TCL_LIBRARY $TCLLIBPATH/tcl8.3'
Can someone please give me any direction for how to solve this issue. I would appreciate the help very much. (Freesurfer version 6 & Ubuntu 16.04)
Thank you all, Idil
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
It is using bash.
Idil ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Tuesday, July 11, 2017 6:30 PM To: Freesurfer support list Subject: Re: [Freesurfer] freeview command error
Hi Idil
do you know what shell you are using in the terminal that you are trying to call freeview from? On Tue, 11 Jul 2017, Yagmur Ozdemir 19 wrote:
Hello, I only followed the steps in the install/download page and installed tcsh because it was not running recon-all. Are you saying that I should set up freeview by sourcing those three files and use the *.csh extension? When opening the terminal again after recon-all to run this I did not do any additional set up. I also remember using .sh when following the steps on the install page. The system does not recognize freeview even when I just use the command alone. Sorry my knowledge pertaining to software use is pretty elementary and there is no one to ask.
Thank you for the help, Idil
From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Tuesday, July 11, 2017 6:03 PM To: Freesurfer support list Subject: Re: [Freesurfer] freeview command error
Hi Idil
how do you setup freesurfer? If you are using bash (and it looks like you are) you should source the *.sh file, not the *.csh. Also, note that you should use T1.mgz not T1/mgz in your freeview command line cheers Bruce On Tue, 11 Jul 2017, Yagmur Ozdemir 19 wrote:
Hello,
I am installing Freesurfer with my limited coding knowledge and this problem with freeview came up when I was trying to view the volumes of recon-ed subject.
lab@lab-ThinkStation-E31:~/Desktop/freesurfer/subjects$ freeview -v practice/mri/T1/mgz No command 'freeview' found, did you mean: Command 'treeview' from package 'treeview' (multiverse) freeview: command not found
I checked and freeview is in the bin, and I even tried to install it according to its file by sourcing tcl_setup and others, but then this error comes up:
lab@lab-ThinkStation-E31:~/Desktop/freesurfer/bin$ source tcl_setup bash: tcl_setup: line 47: syntax error near unexpected token `setenv' bash: tcl_setup: line 47: ` if ( -e $TCLLIBPATH/tcl8.3 ) setenv TCL_LIBRARY $TCLLIBPATH/tcl8.3'
Can someone please give me any direction for how to solve this issue. I would appreciate the help very much. (Freesurfer version 6 & Ubuntu 16.04)
Thank you all, Idil
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
then you shouldn't be sourcing a script that uses setenv. Try sourcing $FREESURFER_HOME/FreeSurferEnv.sh
cheers Bruce On Tue, 11 Jul 2017, Yagmur Ozdemir 19 wrote:
It is using bash.
Idil ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Tuesday, July 11, 2017 6:30 PM To: Freesurfer support list Subject: Re: [Freesurfer] freeview command error
Hi Idil
do you know what shell you are using in the terminal that you are trying to call freeview from? On Tue, 11 Jul 2017, Yagmur Ozdemir 19 wrote:
Hello, I only followed the steps in the install/download page and installed tcsh because it was not running recon-all. Are you saying that I should set up freeview by sourcing those three files and use the *.csh extension? When opening the terminal again after recon-all to run this I did not do any additional set up. I also remember using .sh when following the steps on the install page. The system does not recognize freeview even when I just use the command alone. Sorry my knowledge pertaining to software use is pretty elementary and there is no one to ask.
Thank you for the help, Idil
From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Tuesday, July 11, 2017 6:03 PM To: Freesurfer support list Subject: Re: [Freesurfer] freeview command error
Hi Idil
how do you setup freesurfer? If you are using bash (and it looks like you are) you should source the *.sh file, not the *.csh. Also, note that you should use T1.mgz not T1/mgz in your freeview command line cheers Bruce On Tue, 11 Jul 2017, Yagmur Ozdemir 19 wrote:
Hello,
I am installing Freesurfer with my limited coding knowledge and this problem with freeview came up when I was trying to view the volumes of recon-ed subject.
lab@lab-ThinkStation-E31:~/Desktop/freesurfer/subjects$ freeview -v practice/mri/T1/mgz No command 'freeview' found, did you mean: Command 'treeview' from package 'treeview' (multiverse) freeview: command not found
I checked and freeview is in the bin, and I even tried to install it according to its file by sourcing tcl_setup and others, but then this error comes up:
lab@lab-ThinkStation-E31:~/Desktop/freesurfer/bin$ source tcl_setup bash: tcl_setup: line 47: syntax error near unexpected token `setenv' bash: tcl_setup: line 47: ` if ( -e $TCLLIBPATH/tcl8.3 ) setenv TCL_LIBRARY $TCLLIBPATH/tcl8.3'
Can someone please give me any direction for how to solve this issue. I would appreciate the help very much. (Freesurfer version 6 & Ubuntu 16.04)
Thank you all, Idil
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
-
Bruce Fischl -
Yagmur Ozdemir 19