Subcortical structure segmentation in SEPIA

Starting from v1.2, SEPIA supports several atlas-based subcortical structure segmentation methods, based on non-linear registration using ANTs.

Set-up SEPIA for subcortical structure segmentation

Before using any of these methods, ‘ANTS_HOME’ has to be specified in SpecifyToolboxesDirectory.m or using the Manage Dependency tool in the Utility tab.

The path required for ‘ANTS_HOME’ should be the bin folder of ANTs that contains all the libraries, e.g.,

../_images/ANTs_bin.png

and in the Manage Dependency tool it should be like

../_images/ants_home.png

Note

If you don’t have ANTs, you can still use SEPIA for QSM reconstruction but you can’t use the segmentation methods provided in the Analysis tab.

Then you need to download the atlases from their corresponding online sources. For Mac and Linux users, this can be done by running the shell script download_atlas.sh in the SEPIA_HOME folder. Start a command window and enter the following:

sh download_atlas.sh

../_images/download_atlas_cmd.png

By default, the atlases will be downloaded in SEPIA_HOME/atlas/. Make sure you have enough disk space in your computer and do not alter the location where the atlases stored.

There are currently three atlases supported: