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