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FreeSurfer Tools Tutorial
The tutorial below is meant to introduce you to several tools that are used by the FreeSurfer Development team.
To use any FreeSurfer tool first you must source the FreeSurfer environment that you want to use. To source the development environment, open a terminal window and type the following (if you highlight it and copy it instead, click the middle mouse button to paste in the terminal window):
source /usr/local/freesurfer/nmr-dev-env
To source the stable environment, you would do:
source /usr/local/freesurfer/nmr-std-dev
For the purposes of this tutorial, you can just source the dev version.
Freeview
Freeview is an editing tool similar to Tkmedit described below. It is mostly used to label high resolution ex vivo images and to view diffusion data.
To look at some high res ex vivo data using freeview, do the following:
cd /autofs/space/tensor_010/users/hires/FHS18_ec_031408/mri/flash freeview -v flash20_EC_100um_avg.mgz HP_07112008MG.mgz
This will probably take awhile to load. Once both files are in the left window and the loading bar has stopped, find the 'Color Map option' and switch it from 'Grayscale' to 'Lookup Table'.
You can scroll through the slices by using the 'Page Up' or 'Page Down' button.
Tkmedit