<?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>ScriptingNotes</title><revhistory><revision><revnumber>21</revnumber><date>2013-03-07 21:23:05</date><authorinitials>localhost</authorinitials><revremark>converted to 1.6 markup</revremark></revision><revision><revnumber>20</revnumber><date>2006-10-02 11:24:36</date><authorinitials>IanNimmoSmith</authorinitials></revision><revision><revnumber>19</revnumber><date>2006-10-02 11:14:36</date><authorinitials>IanNimmoSmith</authorinitials></revision><revision><revnumber>18</revnumber><date>2006-10-02 11:13:31</date><authorinitials>IanNimmoSmith</authorinitials></revision><revision><revnumber>17</revnumber><date>2006-10-02 11:12:03</date><authorinitials>IanNimmoSmith</authorinitials></revision><revision><revnumber>16</revnumber><date>2006-10-02 11:11:40</date><authorinitials>IanNimmoSmith</authorinitials></revision><revision><revnumber>15</revnumber><date>2006-10-02 10:47:57</date><authorinitials>IanNimmoSmith</authorinitials></revision><revision><revnumber>14</revnumber><date>2006-10-02 10:46:52</date><authorinitials>IanNimmoSmith</authorinitials></revision><revision><revnumber>13</revnumber><date>2006-10-02 10:45:17</date><authorinitials>IanNimmoSmith</authorinitials></revision><revision><revnumber>12</revnumber><date>2006-10-02 09:30:07</date><authorinitials>IanNimmoSmith</authorinitials></revision><revision><revnumber>11</revnumber><date>2006-10-02 08:35:27</date><authorinitials>IanNimmoSmith</authorinitials></revision><revision><revnumber>10</revnumber><date>2006-10-02 08:18:31</date><authorinitials>IanNimmoSmith</authorinitials></revision><revision><revnumber>9</revnumber><date>2006-10-02 08:17:33</date><authorinitials>IanNimmoSmith</authorinitials></revision><revision><revnumber>8</revnumber><date>2006-10-02 08:15:06</date><authorinitials>IanNimmoSmith</authorinitials></revision><revision><revnumber>7</revnumber><date>2006-10-02 08:13:13</date><authorinitials>IanNimmoSmith</authorinitials></revision><revision><revnumber>6</revnumber><date>2006-10-02 08:12:22</date><authorinitials>IanNimmoSmith</authorinitials></revision><revision><revnumber>5</revnumber><date>2006-10-02 08:08:22</date><authorinitials>IanNimmoSmith</authorinitials></revision><revision><revnumber>4</revnumber><date>2006-10-02 08:07:24</date><authorinitials>IanNimmoSmith</authorinitials></revision><revision><revnumber>3</revnumber><date>2006-10-02 08:07:06</date><authorinitials>IanNimmoSmith</authorinitials></revision><revision><revnumber>2</revnumber><date>2006-10-02 08:05:53</date><authorinitials>IanNimmoSmith</authorinitials></revision><revision><revnumber>1</revnumber><date>2006-10-02 08:04:31</date><authorinitials>IanNimmoSmith</authorinitials></revision></revhistory></articleinfo><section><title>Notes on Scripting, Batching and Tasking for SPM5</title><itemizedlist><listitem><para><emphasis role="strong">Why Script?</emphasis> </para><itemizedlist><listitem><para>A large part of SPM code is complex housekeeping related to files and directories </para></listitem><listitem><para>Tailoring requires attention to these housekeeping matters </para><itemizedlist><listitem><para><emphasis>Have I got the right files?</emphasis> </para></listitem></itemizedlist></listitem><listitem><para>Need to create novel suite of analyses out of a number of core modules </para></listitem><listitem><para>Intercommunication via the SPM.mat structure </para><para><ulink url="https://lsr-wiki-01.mrc-cbu.cam.ac.uk/imaging/ScriptingNotes/imaging/MYV#">MYV</ulink>  </para><para><emphasis role="strong"><ulink url="https://lsr-wiki-01.mrc-cbu.cam.ac.uk/imaging/ScriptingNotes/imaging/AllGorySpmMat#">AllGorySpmMat</ulink></emphasis> </para></listitem></itemizedlist></listitem><listitem><para>Why Batch? </para><itemizedlist><listitem><para>Need to perform same or similar analyses on several datasets </para><para><emphasis role="strong"><ulink url="https://lsr-wiki-01.mrc-cbu.cam.ac.uk/imaging/ScriptingNotes/imaging/BitOfScript#">BitOfScript</ulink></emphasis> </para></listitem><listitem><para><ulink url="https://lsr-wiki-01.mrc-cbu.cam.ac.uk/imaging/ScriptingNotes/imaging/Spm5Tasks#">Spm5Tasks</ulink> </para></listitem><listitem><para>How to access them </para></listitem><listitem><para>What they do </para><itemizedlist><listitem><para><emphasis>Query: how to get jobs saves a .m or .xml files as well as a .mat file? - These options could be useful as these are text files and easier to edit. </emphasis></para></listitem><listitem><para>Job/task manager can be extended </para></listitem><listitem><para>To be clarified: there is some barely undocumented functionality for linking up tasks in sequence so that output of one task become the input to the next. E.g. if you add a normalisation after creating a realignment you will see the option of choosing r* files for normalizing despite the fact that they do not yet exist!</para><emphasis role="strong"> </emphasis></listitem><para><ulink url="https://lsr-wiki-01.mrc-cbu.cam.ac.uk/imaging/ScriptingNotes/imaging/Jobs3#">Jobs3</ulink> </para></itemizedlist></listitem><listitem><para>Other approaches </para><itemizedlist><listitem><para>aa -- Rhodri Cusack's Automatic Analysis modules </para><itemizedlist><listitem><para><ulink url="https://lsr-wiki-01.mrc-cbu.cam.ac.uk/imaging/ScriptingNotes/imaging/AutomaticAnalysisIntroduction#">AutomaticAnalysisIntroduction</ulink> </para></listitem><listitem><para><ulink url="https://lsr-wiki-01.mrc-cbu.cam.ac.uk/imaging/ScriptingNotes/imaging/PetModelAutomation5#">PetModelAutomation5</ulink> </para></listitem></itemizedlist></listitem></itemizedlist></listitem></itemizedlist></listitem></itemizedlist></section></article>