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| == General Linux Help == | == General Linux Help == |
FreeSurfer can be accessed from any Linux computer on the Martinos network. This page will show you how to access the FreeSurfer program and points you towards some tutorials to help learn how to use it.
Accessing FreeSurfer
First, consider if you need access to the stable or development version of FreeSurfer. If you are not sure, you probably want to use the stable version. The development version contains new and untested features.
For whichever version you want, copy and paste a command below into your terminal:
Stable:
source /usr/local/freesurfer/nmr-stable60-env
Development:
source /usr/local/freesurfer/nmr-dev-env
To ensure that worked, type freeview into the command prompt, press enter, and see if FreeView opened. FreeView is a tool that comes with FreeSurfer - it lets you look at the data FreeSurfer creates along with many other files common to MRI research.
Learning how to use FreeSurfer
Here is a recommended way to get up to speed on using FreeSurfer:
If you are not familiar with using a Unix terminal, watch this video: https://www.youtube.com/watch?v=6eJMxh7PlOY
Here is a link to online versions of a FreeSurfer course: https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial
Each lecture has a corresponding video found here: https://www.youtube.com/channel/UCruQerP8aa-gYttXkAcyveA
To get a basic understanding of FreeSurfer it is recommended to go through all course material up to and including "Quality Checking a Recon". From there you can complete the rest to explore different specific functions of FreeSurfer, or select tutorials related to the research you plan to do.
General Linux Help
Examples of scripts and aliases that can make it easier to source, use, and process with FreeSurfer can be found here.
Some basic information on text editors can be found here.
Need help?
There is a wealth of knowledge here on the FSWiki. On the top right hand corner is a search bar - be sure to press the Text option when searching, it offers more results than Topic.
Other resources include an online support archive, see here for more details: https://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferSupport