Hoffman2:Scripts:switch freesurfer

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This page is deprecated. Please see Hoffman2:Modules for more information about CCN-supported software on Hoffman2.

Overview

Use this tool to keep consistent on the FreeSurfer version you are using on Hoffman2.

Usage

Initialization / Switching

If you have never used the tool before, your first usage needs to be to set your FreeSurfer version. e.g.

$ switch_freesurfer -s 5.0.0

would set your FreeSurfer version to 5.0.0

Checking which version is active

You can always check which version you are using with

$ switch_freesurfer -c

Dropping out of the program

And if you no longer wish to use the switch_freesurfer system and instead always use the "current" version maintained on Hoffman2

$ switch_freesurfer -d

will remove you from the program.

NOTE: Whenever you switch FreeSurfer versions or remove your self from the switch_freesurfer program, you need to log in and log out for the changes to take full effect.

Help

Call the program without any options, or with "-h" or "--help" to see the full usage and help information

$ switch_freesurfer
Description: switch_freesurfer easily and cleanly switches between various FreeSurfer versions.

Usage: switch_freesurfer [OPTIONS]
Options:
    -h, --help                       Display this help/usage message
    -v, --verbose                    Verbose output
    -s, --switch VERSION             Designate the appropriate FreeSurfer version. 
                                        If switching between versions, you must log out
                                        then back it to reset up your environment.
                                        Available versions are: 4.0.5, 4.4.0, 5.0.0, 5.1.0
    -c, --check                      Checks for current FreeSurfer version being used
    -d, --delete                     Stops using this system so you instead use the current version
                                        of the tool at all times. You MUST log out and then back
                                        in to properly reset your environment.

Examples: 
        switch_freesurfer -s 4.4.0
        switch_freesurfer --switch 5.0.0
        switch_freesurfer -h
        switch_freesurfer --check