<?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>SpmBatch5</title><revhistory><revision><revnumber>33</revnumber><date>2013-03-18 23:57:06</date><authorinitials>RussellThompson</authorinitials></revision><revision><revnumber>32</revnumber><date>2013-03-18 23:55:51</date><authorinitials>RussellThompson</authorinitials></revision><revision><revnumber>31</revnumber><date>2013-03-18 19:11:14</date><authorinitials>RussellThompson</authorinitials></revision><revision><revnumber>30</revnumber><date>2013-03-18 19:10:36</date><authorinitials>RussellThompson</authorinitials></revision><revision><revnumber>29</revnumber><date>2013-03-18 18:52:01</date><authorinitials>RussellThompson</authorinitials></revision><revision><revnumber>28</revnumber><date>2013-03-18 18:51:43</date><authorinitials>RussellThompson</authorinitials></revision><revision><revnumber>27</revnumber><date>2013-03-18 18:44:51</date><authorinitials>RussellThompson</authorinitials></revision><revision><revnumber>26</revnumber><date>2013-03-18 18:39:52</date><authorinitials>RussellThompson</authorinitials></revision><revision><revnumber>25</revnumber><date>2013-03-18 18:32:41</date><authorinitials>RussellThompson</authorinitials></revision><revision><revnumber>24</revnumber><date>2013-03-18 11:41:10</date><authorinitials>OlafHauk</authorinitials></revision><revision><revnumber>23</revnumber><date>2013-03-18 11:40:14</date><authorinitials>OlafHauk</authorinitials></revision><revision><revnumber>22</revnumber><date>2013-03-18 11:39:40</date><authorinitials>OlafHauk</authorinitials></revision><revision><revnumber>21</revnumber><date>2013-03-18 11:38:34</date><authorinitials>OlafHauk</authorinitials></revision><revision><revnumber>20</revnumber><date>2013-03-18 11:36:08</date><authorinitials>OlafHauk</authorinitials></revision><revision><revnumber>19</revnumber><date>2013-03-18 11:34:13</date><authorinitials>OlafHauk</authorinitials></revision><revision><revnumber>18</revnumber><date>2013-03-18 11:33:33</date><authorinitials>OlafHauk</authorinitials></revision><revision><revnumber>17</revnumber><date>2013-03-18 11:24:49</date><authorinitials>OlafHauk</authorinitials></revision><revision><revnumber>16</revnumber><date>2013-03-18 11:17:34</date><authorinitials>OlafHauk</authorinitials></revision><revision><revnumber>15</revnumber><date>2013-03-18 11:16:29</date><authorinitials>OlafHauk</authorinitials></revision><revision><revnumber>14</revnumber><date>2013-03-18 11:15:31</date><authorinitials>OlafHauk</authorinitials></revision><revision><revnumber>13</revnumber><date>2013-03-07 21:24:01</date><authorinitials>localhost</authorinitials><revremark>converted to 1.6 markup</revremark></revision><revision><revnumber>12</revnumber><date>2008-11-07 13:12:26</date><authorinitials>RikHenson</authorinitials></revision><revision><revnumber>11</revnumber><date>2008-01-21 10:43:29</date><authorinitials>RikHenson</authorinitials></revision><revision><revnumber>10</revnumber><date>2008-01-21 10:40:49</date><authorinitials>RikHenson</authorinitials></revision><revision><revnumber>9</revnumber><date>2008-01-21 09:57:23</date><authorinitials>RikHenson</authorinitials></revision><revision><revnumber>8</revnumber><date>2008-01-21 09:57:08</date><authorinitials>RikHenson</authorinitials></revision><revision><revnumber>7</revnumber><date>2007-05-15 10:40:25</date><authorinitials>AlexandraWoolgar</authorinitials></revision><revision><revnumber>6</revnumber><date>2007-05-15 10:39:30</date><authorinitials>AlexandraWoolgar</authorinitials></revision><revision><revnumber>5</revnumber><date>2007-05-15 10:39:15</date><authorinitials>AlexandraWoolgar</authorinitials></revision><revision><revnumber>4</revnumber><date>2007-05-15 10:38:34</date><authorinitials>AlexandraWoolgar</authorinitials></revision><revision><revnumber>3</revnumber><date>2006-10-26 21:37:57</date><authorinitials>cmbg-cache-2.server.ntli.net</authorinitials></revision><revision><revnumber>2</revnumber><date>2006-07-25 11:57:59</date><authorinitials>devel03.mrc-cbu.cam.ac.uk</authorinitials></revision><revision><revnumber>1</revnumber><date>2006-07-25 11:53:40</date><authorinitials>devel03.mrc-cbu.cam.ac.uk</authorinitials></revision></revhistory></articleinfo><section><title>Batch for SPM5</title><para>Actually, batch for SPM5 is very similar to <ulink url="https://imaging.mrc-cbu.cam.ac.uk/imaging/SpmBatch5/imaging/SpmBatch2#">SpmBatch2</ulink>, with the big exception that you can now save analyses in the GUI to a batch definition file, that can repeat the analysis, and be edited to adapt to another subject or slightly different parameters. </para><para>Nonetheless, if you want to continue working directly with Matlab scripts of calls to spm functions, here are some examples (NB we will not be held responsible for any errors!): </para><itemizedlist><listitem><para>fMRI preprocessing: <ulink url="https://imaging.mrc-cbu.cam.ac.uk/imaging/SpmBatch5/imaging/SpmBatch5?action=AttachFile&amp;do=get&amp;target=batch_spm5_preproc.m">batch_spm5_preproc.m</ulink> </para></listitem><listitem><para>fMRI 1st-level statistics: <ulink url="https://imaging.mrc-cbu.cam.ac.uk/imaging/SpmBatch5/imaging/SpmBatch5?action=AttachFile&amp;do=get&amp;target=batch_spm5_1stlevel.m">batch_spm5_1stlevel.m</ulink> </para></listitem><listitem><para>fMRI 2nd-level statistics (within-subject ANOVA): <ulink url="https://imaging.mrc-cbu.cam.ac.uk/imaging/SpmBatch5/imaging/SpmBatch5?action=AttachFile&amp;do=get&amp;target=batch_spm5_stats_2ndlevel_within_ANOVA.m">batch_spm5_stats_2ndlevel_within_ANOVA.m</ulink> </para></listitem><listitem><para>fMRI 2nd-level statistics (mixed, ie within and between-subject ANOVA) (a bit hacky!): <ulink url="https://imaging.mrc-cbu.cam.ac.uk/imaging/SpmBatch5/imaging/SpmBatch5?action=AttachFile&amp;do=get&amp;target=batch_spm5_stats_2ndlevel_mixed_ANOVA.m">batch_spm5_stats_2ndlevel_mixed_ANOVA.m</ulink> </para></listitem><listitem><para>EEG preprocessing: <ulink url="https://imaging.mrc-cbu.cam.ac.uk/imaging/SpmBatch5/imaging/SpmBatch5?action=AttachFile&amp;do=get&amp;target=batch_spm5_eeg_preproc.m">batch_spm5_eeg_preproc.m</ulink> </para></listitem></itemizedlist><para>More scripts for EEG/MEG preprocessing and source localisation (particularly for the CBU EEG/MEG machines) can be found here: <ulink url="http://imaging.mrc-cbu.cam.ac.uk/meg/SpmAnalysis"/> </para><itemizedlist><listitem><para>Some others <ulink url="https://imaging.mrc-cbu.cam.ac.uk/imaging/SpmBatch5/imaging/SpmBatch5?action=AttachFile&amp;do=get&amp;target=spm2batch.tar.gz">example SPM5 batch scripts</ulink>. </para></listitem></itemizedlist><para>[Some of these scripts are .tar.tar, so from the unix shell you need to rename the file .tar.gz, unzip with gunzip (gunzip [file]), then extract them (tar -xf [file]).] </para></section></article>