<?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>FreesurferInformation</title><revhistory><revision><revnumber>28</revnumber><date>2015-06-15 21:18:46</date><authorinitials>OlafHauk</authorinitials></revision><revision><revnumber>27</revnumber><date>2013-08-06 10:55:39</date><authorinitials>OlafHauk</authorinitials><revremark>Revert to revision 25.</revremark></revision><revision><revnumber>26</revnumber><date>2013-08-06 10:54:02</date><authorinitials>OlafHauk</authorinitials></revision><revision><revnumber>25</revnumber><date>2013-03-07 21:23:04</date><authorinitials>localhost</authorinitials><revremark>converted to 1.6 markup</revremark></revision><revision><revnumber>24</revnumber><date>2012-09-13 14:31:38</date><authorinitials>IanCharest</authorinitials></revision><revision><revnumber>23</revnumber><date>2012-09-12 11:14:04</date><authorinitials>IanCharest</authorinitials></revision><revision><revnumber>22</revnumber><date>2012-03-07 16:59:06</date><authorinitials>YaaraErez</authorinitials></revision><revision><revnumber>21</revnumber><date>2012-03-07 15:00:45</date><authorinitials>IanCharest</authorinitials></revision><revision><revnumber>20</revnumber><date>2012-03-07 15:00:20</date><authorinitials>IanCharest</authorinitials></revision><revision><revnumber>19</revnumber><date>2012-03-07 15:00:08</date><authorinitials>IanCharest</authorinitials></revision><revision><revnumber>18</revnumber><date>2012-03-07 14:59:48</date><authorinitials>IanCharest</authorinitials></revision><revision><revnumber>17</revnumber><date>2012-03-07 14:58:24</date><authorinitials>IanCharest</authorinitials></revision><revision><revnumber>16</revnumber><date>2012-03-07 13:56:18</date><authorinitials>YaaraErez</authorinitials></revision><revision><revnumber>15</revnumber><date>2012-03-07 13:55:46</date><authorinitials>YaaraErez</authorinitials></revision><revision><revnumber>14</revnumber><date>2012-03-07 13:54:36</date><authorinitials>YaaraErez</authorinitials></revision><revision><revnumber>13</revnumber><date>2012-03-07 13:46:47</date><authorinitials>YaaraErez</authorinitials></revision><revision><revnumber>12</revnumber><date>2012-03-07 13:45:56</date><authorinitials>YaaraErez</authorinitials></revision><revision><revnumber>11</revnumber><date>2012-03-07 13:41:50</date><authorinitials>IanCharest</authorinitials></revision><revision><revnumber>10</revnumber><date>2012-03-07 13:39:09</date><authorinitials>IanCharest</authorinitials></revision><revision><revnumber>9</revnumber><date>2012-03-07 13:38:52</date><authorinitials>IanCharest</authorinitials></revision><revision><revnumber>8</revnumber><date>2012-03-07 13:12:26</date><authorinitials>IanCharest</authorinitials></revision><revision><revnumber>7</revnumber><date>2012-03-07 13:11:50</date><authorinitials>IanCharest</authorinitials></revision><revision><revnumber>6</revnumber><date>2008-03-14 15:22:01</date><authorinitials>DanielWakeman</authorinitials></revision><revision><revnumber>5</revnumber><date>2008-03-14 15:19:28</date><authorinitials>DanielWakeman</authorinitials></revision><revision><revnumber>4</revnumber><date>2007-05-05 10:42:01</date><authorinitials>host86-148-55-122.range86-148.btcentralplus.com</authorinitials></revision><revision><revnumber>3</revnumber><date>2007-05-05 10:41:39</date><authorinitials>host86-148-55-122.range86-148.btcentralplus.com</authorinitials></revision><revision><revnumber>2</revnumber><date>2007-05-05 10:41:19</date><authorinitials>host86-148-55-122.range86-148.btcentralplus.com</authorinitials></revision><revision><revnumber>1</revnumber><date>2007-05-05 10:41:08</date><authorinitials>host86-148-55-122.range86-148.btcentralplus.com</authorinitials></revision></revhistory></articleinfo><section><title>Freesurfer</title><itemizedlist><listitem override="none"><para><ulink url="http://surfer.nmr.mgh.harvard.edu/">freesurfer homepage</ulink> </para><para><ulink url="http://surfer.nmr.mgh.harvard.edu/fswiki">freesurfer wiki</ulink> </para></listitem></itemizedlist><para>From the website: </para><itemizedlist><listitem override="none"><para>Freesurfer is a set of automated tools for reconstruction of the brain’s cortical surface from structural MRI data, and overlay of functional MRI data onto the reconstructed surface. </para></listitem></itemizedlist><para>You can now use Freesurfer 5.1 at the CBU. </para><para>To run freesurfer 5.1 on the CBU systems, run the following from the linux prompt, or put this line into your <code>.cshrc</code> file: </para><screen><![CDATA[alias freesurfer 'setenv FREESURFER_HOME /imaging/local/software/freesurfer/5.1.0; setenv SUBJECTS_DIR /imaging/yourusername/freesurfer_data; source $FREESURFER_HOME/SetUpFreesurfer.csh']]></screen><para>If you would rather use the previous version (4.3.0) just type the following command: </para><screen><![CDATA[freesurfer_4.3.0]]></screen><para>This will setup freesurfer with load balancing.   </para><para><emphasis role="strong">Important</emphasis>: To use the graphical tools use a <ulink url="http://imaging.mrc-cbu.cam.ac.uk/imaging/ImagingComputingDevelopments">vncserver.glx</ulink> session. </para><para>Or you can type this in the terminal to set it up with load balancing: </para><screen><![CDATA[freesurfer_5.1.0]]></screen></section></article>