<?xml version="1.0" encoding="utf-8"?><!DOCTYPE article  PUBLIC '-//OASIS//DTD DocBook XML V4.4//EN'  'http://www.docbook.org/xml/4.4/docbookx.dtd'><article><articleinfo><title>UsingFreesurfer</title><revhistory><revision><revnumber>3</revnumber><date>2013-03-07 21:23:05</date><authorinitials>localhost</authorinitials><revremark>converted to 1.6 markup</revremark></revision><revision><revnumber>2</revnumber><date>2008-02-07 11:11:30</date><authorinitials>DanielWakeman</authorinitials></revision><revision><revnumber>1</revnumber><date>2007-05-08 14:57:27</date><authorinitials>devel03.mrc-cbu.cam.ac.uk</authorinitials></revision></revhistory></articleinfo><section><title>Using Freesurfer</title><para>See <ulink url="https://lsr-wiki-01.mrc-cbu.cam.ac.uk/imaging/UsingFreesurfer/imaging/FreesurferInformation#">FreesurferInformation</ulink> for details on running the software, and help links. </para><para>These are just some notes to remind me what I am doing as I go. </para><itemizedlist><listitem><para>set freesurfer data directory </para></listitem><listitem><para>run recon-all with nifti image as input </para></listitem></itemizedlist><para><ulink url="https://lsr-wiki-01.mrc-cbu.cam.ac.uk/imaging/UsingFreesurfer/imaging/DanStructurals#">DanStructurals</ulink> </para></section></article>