<?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>SpmInformation</title><revhistory><revision><revnumber>39</revnumber><date>2013-04-24 13:41:20</date><authorinitials>TiborAuer</authorinitials></revision><revision><revnumber>38</revnumber><date>2013-03-07 21:22:55</date><authorinitials>localhost</authorinitials><revremark>converted to 1.6 markup</revremark></revision><revision><revnumber>37</revnumber><date>2009-11-02 12:10:05</date><authorinitials>MattDavis</authorinitials></revision><revision><revnumber>36</revnumber><date>2009-11-02 12:08:49</date><authorinitials>MattDavis</authorinitials></revision><revision><revnumber>35</revnumber><date>2009-11-02 12:08:30</date><authorinitials>MattDavis</authorinitials></revision><revision><revnumber>34</revnumber><date>2009-11-02 12:04:09</date><authorinitials>MattDavis</authorinitials></revision><revision><revnumber>33</revnumber><date>2009-11-02 12:03:30</date><authorinitials>MattDavis</authorinitials></revision><revision><revnumber>32</revnumber><date>2009-10-16 13:25:34</date><authorinitials>RhodriCusack</authorinitials></revision><revision><revnumber>31</revnumber><date>2009-10-16 13:24:45</date><authorinitials>RhodriCusack</authorinitials></revision><revision><revnumber>30</revnumber><date>2009-10-16 13:24:25</date><authorinitials>RhodriCusack</authorinitials></revision><revision><revnumber>29</revnumber><date>2009-10-16 13:23:34</date><authorinitials>RhodriCusack</authorinitials></revision><revision><revnumber>28</revnumber><date>2009-10-16 13:21:37</date><authorinitials>RhodriCusack</authorinitials></revision><revision><revnumber>27</revnumber><date>2009-10-16 13:17:23</date><authorinitials>RhodriCusack</authorinitials></revision><revision><revnumber>26</revnumber><date>2008-08-29 14:22:09</date><authorinitials>RikHenson</authorinitials></revision><revision><revnumber>25</revnumber><date>2008-02-15 17:09:28</date><authorinitials>RikHenson</authorinitials></revision><revision><revnumber>24</revnumber><date>2008-02-15 17:08:00</date><authorinitials>RikHenson</authorinitials></revision><revision><revnumber>23</revnumber><date>2008-02-15 17:00:14</date><authorinitials>RikHenson</authorinitials></revision><revision><revnumber>22</revnumber><date>2007-07-25 09:36:22</date><authorinitials>RhodriCusack</authorinitials></revision><revision><revnumber>21</revnumber><date>2007-03-09 20:27:41</date><authorinitials>callosum.BIC.Berkeley.EDU</authorinitials></revision><revision><revnumber>20</revnumber><date>2007-03-09 20:21:09</date><authorinitials>callosum.BIC.Berkeley.EDU</authorinitials></revision><revision><revnumber>19</revnumber><date>2007-03-09 20:20:55</date><authorinitials>callosum.BIC.Berkeley.EDU</authorinitials></revision><revision><revnumber>18</revnumber><date>2006-10-09 15:10:31</date><authorinitials>RhodriCusack</authorinitials></revision><revision><revnumber>17</revnumber><date>2006-10-09 15:10:19</date><authorinitials>RhodriCusack</authorinitials></revision><revision><revnumber>16</revnumber><date>2006-08-16 17:05:09</date><authorinitials>cmbg-cache-2.server.ntli.net</authorinitials></revision><revision><revnumber>15</revnumber><date>2006-08-16 16:37:39</date><authorinitials>cmbg-cache-2.server.ntli.net</authorinitials></revision><revision><revnumber>14</revnumber><date>2006-08-16 13:37:14</date><authorinitials>RhodriCusack</authorinitials></revision><revision><revnumber>13</revnumber><date>2006-08-16 13:20:24</date><authorinitials>RhodriCusack</authorinitials></revision><revision><revnumber>12</revnumber><date>2006-08-16 11:03:20</date><authorinitials>RhodriCusack</authorinitials></revision><revision><revnumber>11</revnumber><date>2006-08-16 10:28:55</date><authorinitials>RhodriCusack</authorinitials></revision><revision><revnumber>10</revnumber><date>2006-08-16 10:21:32</date><authorinitials>RhodriCusack</authorinitials></revision><revision><revnumber>9</revnumber><date>2006-08-16 09:49:49</date><authorinitials>RhodriCusack</authorinitials></revision><revision><revnumber>8</revnumber><date>2006-08-16 09:49:04</date><authorinitials>RhodriCusack</authorinitials></revision><revision><revnumber>7</revnumber><date>2006-07-24 17:13:20</date><authorinitials>cmbg-cache-2.server.ntli.net</authorinitials></revision><revision><revnumber>6</revnumber><date>2006-07-24 15:37:21</date><authorinitials>cmbg-cache-2.server.ntli.net</authorinitials></revision><revision><revnumber>5</revnumber><date>2006-07-24 09:10:27</date><authorinitials>devel03.mrc-cbu.cam.ac.uk</authorinitials></revision><revision><revnumber>4</revnumber><date>2006-07-21 12:11:39</date><authorinitials>cmbg-cache-2.server.ntli.net</authorinitials></revision><revision><revnumber>3</revnumber><date>2006-07-04 16:27:27</date><authorinitials>cmbg-cache-2.server.ntli.net</authorinitials></revision><revision><revnumber>2</revnumber><date>2006-07-04 16:27:04</date><authorinitials>cmbg-cache-2.server.ntli.net</authorinitials></revision><revision><revnumber>1</revnumber><date>2006-07-04 16:25:29</date><authorinitials>cmbg-cache-2.server.ntli.net</authorinitials></revision></revhistory></articleinfo><para>This is a practical guide to using SPM. If you're after theory, you might want the Analysis Principles section from the menu on the left. </para><section><title>Getting started with SPM</title><itemizedlist><listitem><para><ulink url="https://imaging.mrc-cbu.cam.ac.uk/imaging/SpmInformation/imaging/SpmVersions#">SpmVersions</ulink> - and how to launch them at the CBU </para></listitem><listitem><para><ulink url="https://imaging.mrc-cbu.cam.ac.uk/imaging/SpmInformation/imaging/SpmManuals#">SpmManuals</ulink> </para></listitem></itemizedlist></section><section><title>SPM tips and tools</title><itemizedlist><listitem><para><ulink url="http://www.sph.sc.edu/comd/rorden/mritut.html">Normalizing anatomical MRI scans of damaged brains</ulink> using SPM and MRIcro. </para></listitem><listitem><para><ulink url="https://imaging.mrc-cbu.cam.ac.uk/imaging/SpmInformation/imaging/MaskedEpiNormalization#">MaskedEpiNormalization</ulink> - using the EPIs for spatial normalization. </para></listitem><listitem><para><ulink url="https://imaging.mrc-cbu.cam.ac.uk/imaging/SpmInformation/imaging/SpmPlottingAdjustedData#">SpmPlottingAdjustedData</ulink> </para></listitem><listitem><para><ulink url="https://imaging.mrc-cbu.cam.ac.uk/imaging/SpmInformation/imaging/DisplaySlices#">DisplaySlices</ulink> - display multiple image slices with activation data using matlab / SPM </para></listitem><listitem><para>Changing the location of images in an SPM design with <ulink url="https://imaging.mrc-cbu.cam.ac.uk/imaging/SpmInformation/imaging/SpmAnaCd#">SpmAnaCd</ulink> </para></listitem><listitem><para><ulink url="https://imaging.mrc-cbu.cam.ac.uk/imaging/SpmInformation/imaging/SpmTips#">SpmTips</ulink> - not otherwise classified tips and fixes </para></listitem><listitem><para><ulink url="https://imaging.mrc-cbu.cam.ac.uk/imaging/SpmInformation/imaging/TrimmingImages#">TrimmingImages</ulink> using SPM </para></listitem></itemizedlist></section><section><title>Automating SPM</title><itemizedlist><listitem><para><ulink url="https://imaging.mrc-cbu.cam.ac.uk/imaging/SpmInformation/imaging/AA#">aa</ulink> - automating SPM analyses </para></listitem><listitem><para><ulink url="https://imaging.mrc-cbu.cam.ac.uk/imaging/SpmInformation/imaging/SpmBatch#">SpmBatch</ulink> - batching SPM jobs </para></listitem></itemizedlist></section><section><title>Programming with SPM</title><itemizedlist><listitem><para><ulink url="https://imaging.mrc-cbu.cam.ac.uk/imaging/SpmInformation/imaging/SpmGraphics#">SpmGraphics</ulink> - using the SPM output graphics for making figures </para></listitem><listitem><para><ulink url="https://imaging.mrc-cbu.cam.ac.uk/imaging/SpmInformation/imaging/BasicProgrammingWithSpm#">BasicProgrammingWithSpm</ulink> </para></listitem></itemizedlist></section><section><title>Benchmarking SPM</title><itemizedlist><listitem><para><ulink url="https://imaging.mrc-cbu.cam.ac.uk/imaging/SpmInformation/imaging/SpmWithPentium4#">SpmWithPentium4</ulink> - tuning SPM for the Pentium 4 chip </para></listitem><listitem><para><ulink url="http://gnumex.sourceforge.net/">Compiling SPM on Windows</ulink> </para></listitem><listitem><para><ulink url="https://imaging.mrc-cbu.cam.ac.uk/imaging/SpmInformation/imaging/SpmBenchmarks#">SpmBenchmarks</ulink> - benchmarks from machines running SPM </para></listitem><listitem><para><ulink url="https://imaging.mrc-cbu.cam.ac.uk/imaging/SpmInformation/imaging/TestsNewConfigJuly2009#">TestsNewConfigJuly2009</ulink> - testing different configurations of Linux with various neuroimaging packages </para></listitem></itemizedlist></section><section><title>Recent Updates</title><section><title>2009/08/25 Default spm 8 to Matlab2009a</title><screen><![CDATA[spm 8]]></screen><para>now defaults to matlab2009a as this offers the full functionality </para><para>Also, you may do commands like </para><screen><![CDATA[spm 5 matlab2009a]]></screen><para>[RC] </para></section><section><title>2008/11/26 Update Juelich's Anatomy toolbox for SPM 5</title><para>Obtained a new pre-release version of the toolbox, containing new maps for the parietal lobe. Replaced the old version [RC] </para></section><section><title>2008/10/6 Installed Juelich's Anatomy toolbox into SPM 5</title><para>[RC] </para></section><section><title>2008/08/13 Added highmemory switch to spm</title><para>If you launch spm with <!--transclusion is not implemented in DocBook formatter-->spm highmemory<!--transclusion is not implemented in DocBook formatter--> you will be sent to a machine with 16 GB of RAM. </para><para>[RC] </para></section></section><section><title>2008/02/07 Added function HeadMask.m to /imaging/local/spm/common_spm5andabove</title><para>This function attempts to mask out the vitamin E capsules from T1 weighted structurals. This is useful before producing a scalp mesh, which may otherwise be distorted. It has been tested on seven subjects, never removing anything it shouldn't, and successfully removing the vitamin E capsules in six of the seven cases. (Including one patient with lesions; use at own risk; does NOT seem to improve normalisation to MNI space.) </para><para>[<ulink url="https://imaging.mrc-cbu.cam.ac.uk/imaging/SpmInformation/imaging/DannyMitchell#">DannyMitchell</ulink>] </para><section><title>2008/02/06 Patched spm_getSPM manually</title><para>Fixed bug when saving design matrix from contrast manager as identified by Catherine Marie-Longtin, and solved by Ferath Kherif </para><screen><![CDATA[put
cd(SPM.swd) at line 200,
just after the code : SPM.swd = swd; at line 199.]]></screen><para>[RC] </para></section></section><section><title>Getting more help</title><para>For help on SPM and other analysis topics, see <ulink url="https://imaging.mrc-cbu.cam.ac.uk/imaging/SpmInformation/imaging/AnalysisHelp#">AnalysisHelp</ulink> </para></section></article>