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: zkaufman@nmr.mgh.harvard.edu To: pablonajt@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.
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 10.6.8Thank you so much,Pablo
Date: Tue, 11 Jun 2013 11:02:26 -0400 From: zkaufman@nmr.mgh.harvard.edu To: pablonajt@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: zkaufman@nmr.mgh.harvard.edu To: pablonajt@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
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: zkaufman@nmr.mgh.harvard.edu To: pablonajt@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: zkaufman@nmr.mgh.harvard.edu To: pablonajt@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
freesurfer@nmr.mgh.harvard.edu
-
pablo najt -
Z K -
zkaufman＠nmr.mgh.harvard.edu