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Converting a Skull Stripped Brain to a mask

Written by Owen Phillips, email with questions or comments.

This tutorial will show how to use any analyze (img/hdr) file and convert it to a mask. You will need a skull stripped brain (from TraceWalker, for example) as your starting file (see below).

In this first section I will run things directly on inire and the second section I will run it on the LONI Pipeline.

1. Connect to inire via a terminal:
   ssh -X user@inire.loni.ucla.edu or open a unix terminal on your local machine.

   

2. To binarize your skull stripped volume, you will use avwmaths "input" -bin "output"
   

   

3. You will now have a binarized mask that you can load in brain suite as a label (left). On the right, you can see the mask loaded in BrainSuite by itself.

   

Notes:

There are other ways of doing this including "binarize" and "mincmath". binarize is part of the AIR package, and mincmath comes with the MNI tools package. Type binarize or mincmath -help at the command line (on inire, for example) for help on how to use these tools.

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