Applied Neurobiological Imaging, Dr. Katherine L. Narr

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Converting a Skull Stripped Brain to a mask

Written by Owen Phillips, email email ophillip at loni dot ucla dot edu 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).

skull stripped volume

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 or open a unix terminal on your local machine.

    connect to inire

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

    run avwmaths on the command line

  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.

    binarized mask loaded as a label on top of the skull stripped volume binarized mask


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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