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| There are three main internal distributions of FreeSurfer available at the NMR Center. To use a distribution, set your FREESURFER_HOME environment variable to the directory of the distribution and then source the Free``Surfer``Env.csh file in that distribution. For example: |
All computers on the NMR network should have the directory {{{/usr/local/freesurfer}}}. Inside there, you will see the files nmr-std-env and nmr-dev-env. Sourcing these will set up your environment to use the stable or dev version, respectively. For example, to use the stable version, which is what most users should do, use the following setup command: {{{ $ source /usr/local/freesurfer/nmr-std-env}}} You should see the prompt change to {{{(nmr-std-env)}}} and your environment should then be set up to run FreeSurfer. Note that the programs may appear to be in a different location: {{{$ which tkmedit /space/birn/50/freesurfer/rh7.3/beta/bin/tkmedit}}} That's OK, because {{{/usr/local/freesurfer}}} is actually a link to a platform specific version that resides in a different directory, much like how {{{/usr/pubsw}}} works. If you don't know what this means, don't worry. Your {{{FREESURFER_HOME}}} will actually be {{{/usr/local/freesurfer/beta}}} or {{{/usr/local/freesurfer/dev}}}, so if you'd like to set F{{{REESURFER_HOME}}} manually, you can still do so. You can suppress output from sourcing these scripts with the {{{FS_FREESURFERENV_NO_OUTPUT}}} environment variable: {{{ setenv FS_FREESURFERENV_NO_OUTPUT}}} You can keep the prompt from changing to {{{(nmr-std-env)}}} or {{{(nmr-dev-env)}}} by setting {{{FSENV_KEEP_PROMPT}}}: {{{ setenv FSENV_KEEP_PROMPT}}} These are the older versions that are still available for compatibility, but will soon be removed. For instructions on how to make a local copy of one of these versions for your private use, see MakingPrivateCopiesOfObseoleteDistributions. There are three older internal distributions of FreeSurfer available at the NMR Center. To use a distribution, set your FREESURFER_HOME environment variable to the directory of the distribution and then source the Free``Surfer``Env.csh file in that distribution. For example: |
All computers on the NMR network should have the directory /usr/local/freesurfer. Inside there, you will see the files nmr-std-env and nmr-dev-env. Sourcing these will set up your environment to use the stable or dev version, respectively. For example, to use the stable version, which is what most users should do, use the following setup command:
$ source /usr/local/freesurfer/nmr-std-env
You should see the prompt change to (nmr-std-env) and your environment should then be set up to run FreeSurfer. Note that the programs may appear to be in a different location:
{{{$ which tkmedit /space/birn/50/freesurfer/rh7.3/beta/bin/tkmedit}}}
That's OK, because /usr/local/freesurfer is actually a link to a platform specific version that resides in a different directory, much like how /usr/pubsw works. If you don't know what this means, don't worry.
Your FREESURFER_HOME will actually be /usr/local/freesurfer/beta or /usr/local/freesurfer/dev, so if you'd like to set FREESURFER_HOME manually, you can still do so.
You can suppress output from sourcing these scripts with the FS_FREESURFERENV_NO_OUTPUT environment variable:
setenv FS_FREESURFERENV_NO_OUTPUT
You can keep the prompt from changing to (nmr-std-env) or (nmr-dev-env) by setting FSENV_KEEP_PROMPT:
setenv FSENV_KEEP_PROMPT
These are the older versions that are still available for compatibility, but will soon be removed. For instructions on how to make a local copy of one of these versions for your private use, see MakingPrivateCopiesOfObseoleteDistributions.
There are three older internal distributions of FreeSurfer available at the NMR Center. To use a distribution, set your FREESURFER_HOME environment variable to the directory of the distribution and then source the FreeSurferEnv.csh file in that distribution. For example:
setenv FREESURFRER_HOME ~inverse/freesurfer_alpha source $FREESURFER_HOME/FreeSurferEnv.csh
Note that you may still have to set up your path. Be sure you are using the right binaries with the which command.
See