Pablo,Attached are the original SetUpFreeSurfer.csh and SetUpFreeSurfer.sh files that come with the Freesurfer5.3 installation package.
-Zeke On 06/11/2013 02:56 PM, pablo najt wrote:
Thank you for your answer. There is another issue I am needing help with. As I have edited the .csh file from FreeSurfer I am not able to make it work any more. Is there a way to have a copy of the SetUpFreeSurfer.csh? I have downloaded the last version of Freesurfer for OSX 10.6.8 Thank you so much, Pablo > Date: Tue, 11 Jun 2013 11:02:26 -0400 > From: zkauf...@nmr.mgh.harvard.edu > To: pablon...@hotmail.com > CC: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] environment variable FREESURFER_HOME > > Pablo, > > The .cshrc and .bashrc files we are referring to are not Freesurfer files > and do not come with the Freesurfer distribution. They are files that can > (although not always) exist in the home directory of your computer. > > Do not modify the the .csh or .sh files that come with Freesurfer. That is > for the expert user. > > If you want to use Freesurfer just open a command line and type the > following: > > (if using csh) > setenv FREESURFER_HOME Applications/freesurfer > source $FREESURFER_HOME/SetUpFreeSurfer.csh > > (if using bash) > export FREESURFER_HOME=/Applications/freesurfer > source $FREESURFER_HOME/SetUpFreeSurfer.sh > > If you dont want to type these commands everytime you want to start using > freesurfer than you can add these lines to your .csh and .bashrc *in your > home directory*. If those files do not exist than you may create them *in > your home directory* and simply add those two lines to the file. > > -Zeke > > > > > > Dear Freesurfer experts, > > I am trying to install free surfer. > > It seems that my downloaded version does not have a .cshrc file. I only > > have an .sh and .csh file. > > All the edits (i.e.,setenv FREESURFER_HOME Applications/freesurfer/ source > > Applications/freesurfer/SetUpFreeSurfer.csh) that I tried to the .csh file > > give me "command not found". > > > > Any suggestion would be highly appreciated. > > Pablo > > > > > > > Thank you for your response. > > It seems that my downloaded version does not have a .cshrc file. I only > > have an .sh and a .csh. > > What would you recommend to do? Should I reinstall FreeSurfer? > > Thanks. > > Pablo > > > >> Date: Fri, 7 Jun 2013 18:16:56 -0400 > >> From: zkauf...@nmr.mgh.harvard.edu > >> To: pablon...@hotmail.com > >> Subject: Re: [Freesurfer] environment variable FREESURFER_HOME > >> > >> There should be a file called ".cshrc" in your home directory. Add the > >> two lines to that file. > >> > >> -Zeke > >> > >> On 06/07/2013 05:53 PM, pablo najt wrote: > >> > Can anyone advice me on how to set the environment variable > >> > FREESURFER_HOME for installing it in OS X 10.6.8 (with XQuartz > >> installed)? > >> > > >> > My directory for Freesurfer:*/Applications/freesurfer* > >> > * > >> > * > >> > I know I also have to add: > >> > > >> > setenv FREESURFER_HOME /Applications/freesurfer > >> > > >> > source $FREESURFER_HOME/SetUpFreeSurfer.csh > >> > But I am not sure where exactly I should add these lines. > >> > > >> > Do I need to edit the .csh file in Freesurfer. > >> > > >> > How should I do this? using Text Edit from apple would work? > >> > Thanks, > >> > Pablo > >> > > >> > > >> > > >> > > >> > _______________________________________________ > >> > Freesurfer mailing list > >> > Freesurfer@nmr.mgh.harvard.edu > >> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >> > > >> > >> > >> 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. > >> > > > > _______________________________________________ > 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
SetUpFreeSurfer.csh
Description: C-Shell script
SetUpFreeSurfer.sh
Description: application/shellscript
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