<?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>AlbertIntExtPaper</title><revhistory><revision><revnumber>18</revnumber><date>2013-03-08 10:28:26</date><authorinitials>localhost</authorinitials><revremark>converted to 1.6 markup</revremark></revision><revision><revnumber>17</revnumber><date>2008-06-30 12:11:25</date><authorinitials>customer11311.pool1.Liverpool-MER6166-BAS0001.orangehomedsl.co.uk</authorinitials></revision><revision><revnumber>16</revnumber><date>2008-06-30 11:57:36</date><authorinitials>customer11311.pool1.Liverpool-MER6166-BAS0001.orangehomedsl.co.uk</authorinitials></revision><revision><revnumber>15</revnumber><date>2008-06-29 22:50:26</date><authorinitials>customer11311.pool1.Liverpool-MER6166-BAS0001.orangehomedsl.co.uk</authorinitials></revision><revision><revnumber>14</revnumber><date>2008-06-29 13:11:58</date><authorinitials>customer11311.pool1.Liverpool-MER6166-BAS0001.orangehomedsl.co.uk</authorinitials></revision><revision><revnumber>13</revnumber><date>2008-06-29 13:08:29</date><authorinitials>customer11311.pool1.Liverpool-MER6166-BAS0001.orangehomedsl.co.uk</authorinitials></revision><revision><revnumber>12</revnumber><date>2008-06-29 13:07:37</date><authorinitials>customer11311.pool1.Liverpool-MER6166-BAS0001.orangehomedsl.co.uk</authorinitials></revision><revision><revnumber>11</revnumber><date>2008-06-29 13:06:15</date><authorinitials>customer11311.pool1.Liverpool-MER6166-BAS0001.orangehomedsl.co.uk</authorinitials></revision><revision><revnumber>10</revnumber><date>2008-06-28 21:07:05</date><authorinitials>customer11311.pool1.Liverpool-MER6166-BAS0001.orangehomedsl.co.uk</authorinitials></revision><revision><revnumber>9</revnumber><date>2008-06-28 17:00:37</date><authorinitials>customer11311.pool1.Liverpool-MER6166-BAS0001.orangehomedsl.co.uk</authorinitials></revision><revision><revnumber>8</revnumber><date>2008-06-28 15:39:47</date><authorinitials>customer11311.pool1.Liverpool-MER6166-BAS0001.orangehomedsl.co.uk</authorinitials></revision><revision><revnumber>7</revnumber><date>2008-06-28 15:39:35</date><authorinitials>customer11311.pool1.Liverpool-MER6166-BAS0001.orangehomedsl.co.uk</authorinitials></revision><revision><revnumber>6</revnumber><date>2008-06-28 13:57:18</date><authorinitials>customer11311.pool1.Liverpool-MER6166-BAS0001.orangehomedsl.co.uk</authorinitials></revision><revision><revnumber>5</revnumber><date>2008-06-28 13:50:59</date><authorinitials>customer11311.pool1.Liverpool-MER6166-BAS0001.orangehomedsl.co.uk</authorinitials></revision><revision><revnumber>4</revnumber><date>2008-06-28 13:48:34</date><authorinitials>customer11311.pool1.Liverpool-MER6166-BAS0001.orangehomedsl.co.uk</authorinitials></revision><revision><revnumber>3</revnumber><date>2008-06-28 13:44:36</date><authorinitials>customer11311.pool1.Liverpool-MER6166-BAS0001.orangehomedsl.co.uk</authorinitials></revision><revision><revnumber>2</revnumber><date>2008-06-28 13:34:42</date><authorinitials>customer11311.pool1.Liverpool-MER6166-BAS0001.orangehomedsl.co.uk</authorinitials></revision><revision><revnumber>1</revnumber><date>2008-06-28 13:31:13</date><authorinitials>customer11311.pool1.Liverpool-MER6166-BAS0001.orangehomedsl.co.uk</authorinitials></revision></revhistory></articleinfo><section><title>Working notes on Albert, Ivry, Miall?, Brett paper</title><para>Codename <emphasis role="strong">rechoicey</emphasis> </para><section><title>State of the data</title><section><title>Locations</title><itemizedlist><listitem><para>avalon.bham.ac.uk (behind a firewall) at <code>/home/avalon/albertn/data/rechoicey</code> </para></listitem><listitem><para>Neil's external disk at home, accessible, from Linux, as <code>mount -t cifs //192.168.1.117/Neil/Experiments/FMRI/Choicey /mnt/neil -o user=name,password=pass</code> </para></listitem></itemizedlist><para>We'll call this file location CHOICEYROOT </para></section></section><section><title>Behavioral data</title><itemizedlist><listitem><para>Within <code>CHIOCEYROOT/behavior</code> there is a summary sheet called <code>Choicey_behavior.xls</code>. This file is the file exported after merging the individual eprime data (edat) files. </para></listitem><listitem><para>Default E-Prime output files are located in <code>CHOICEYROOT/behavior/edat/&lt;subjectid&gt;</code>: </para><itemizedlist><listitem><para>Individual edat files exist for each run for each subject.  </para></listitem><listitem><para>Individual run-time e-prime log files (text files). <emphasis role="strong">missing .txt</emphasis>: subjects 35-37. </para></listitem></itemizedlist></listitem><listitem><para>User created outupt files are located in <code>CHOCEYROOT/&lt;subjectid&gt;/refs</code>:  </para><itemizedlist><listitem><para>the event timing log files (.dat) that is ouput from e-prime.  </para></listitem><listitem><para>the .ref file which has converted the above into info to <code>groovy_batch</code> models. </para></listitem><listitem><para>the .rtm file (reaction time matched reference file) for <code>groovy_batch</code> models. </para></listitem></itemizedlist></listitem><listitem><para>Within the directory, directory above, eprime files in <code>CHOICEYROOT/data/behavior</code> </para></listitem><listitem><para>edat files for all runs, txt files (with identical information) for all but subjects 35-37. Edat and equivalent txt files record full log of events in eprime.   </para></listitem><listitem><para>There were also .dat files written out from the script, with information selected by the script. These are in <code>CHOICEYROOT/data/refs/&lt;subjectid&gt;</code>  </para></listitem><listitem><para>Matlab processed versions of these files became the .ref files for the analysis - <code>CHOICEYROOT/&lt;subjectid&gt;/refs</code> </para></listitem><listitem><para><emphasis>NOTES:</emphasis>  Subject 29OM needs to have recovery of the behavioral data and also will need to get the <ulink url="https://imaging.mrc-cbu.cam.ac.uk/methods/AlbertIntExtPaper/methods/PostFix#">PostFix</ulink>.<ulink url="https://imaging.mrc-cbu.cam.ac.uk/methods/AlbertIntExtPaper/methods/OnsetDelay#">OnsetDelay</ulink> and timing mode for <ulink url="https://imaging.mrc-cbu.cam.ac.uk/methods/AlbertIntExtPaper/methods/PostFix#">PostFix</ulink> and its logging of &quot;mouse&quot; responses. </para></listitem></itemizedlist><para>Some data, and code to analyze the files above in <ulink url="http://imaging.mrc-cbu.cam.ac.uk/svn/choiceyana/devel"/> </para></section><section><title>Subjects</title><orderedlist numeration="arabic"><listitem><para>21AW </para></listitem><listitem><para>22JS </para></listitem><listitem><para>23JX </para></listitem><listitem><para>24EC </para></listitem><listitem><para>25AM </para></listitem><listitem><para>26ZD </para></listitem><listitem><para>27FR </para></listitem><listitem><para>28MH </para></listitem><listitem><para>29om (EXCLUDE <emphasis role="strong">?</emphasis>: didn't finish experiment - 4 sessions) </para></listitem><listitem><para>30AP </para></listitem><listitem><para>31FP (EXCLUDE <emphasis role="strong">?</emphasis>: didn't vary self selection) </para></listitem><listitem><para>32AW </para></listitem><listitem><para>33LA </para></listitem><listitem><para>34TJ </para></listitem><listitem><para>35NL </para></listitem><listitem><para>36HW (EXCLUDE <emphasis role="strong">?</emphasis>: Image artifact? earings?) </para></listitem><listitem><para>37MH </para></listitem></orderedlist></section><section><title>Literature review</title><para>All studies using PET or FMRI to study internal / external selection.  Studies looking at internal / external timing excluded, unless they independently look at selection.   For each paper: </para><itemizedlist><listitem><para>Thumbnail description of task.  Concentrating on nature of baseline, any potential difficulty confounds, whether preparation matched.  Note differences in task RTs </para></listitem><listitem><para>For each subtraction, note activation coordinates and Z / t scores in medial premotor cortex (SMA, preSMA, anterior cingulate (Z &gt; 0, abs(X) &lt; 10, Y &gt; -20?), premotor cortex (dorsal or ventral).   </para></listitem><listitem><para>Note modality, template, coordinate frame / normalization (MNI, Talairach, etc) </para></listitem><listitem><para>Results (as reported, including negatively) of Internal - Rest, External - Rest, Internal - External , External - Internal.  Note lack of report as well as 'no significant activation'.  Note threshold used for each.  </para></listitem></itemizedlist><para>See <ulink url="https://imaging.mrc-cbu.cam.ac.uk/methods/AlbertIntExtPaper/methods/DefiningSma#">DefiningSma</ulink> </para></section></section></article>