<?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>BitOfScript</title><revhistory><revision><revnumber>6</revnumber><date>2013-03-07 21:22:56</date><authorinitials>localhost</authorinitials><revremark>converted to 1.6 markup</revremark></revision><revision><revnumber>5</revnumber><date>2006-10-03 10:53:11</date><authorinitials>IanNimmoSmith</authorinitials></revision><revision><revnumber>4</revnumber><date>2006-10-03 10:48:56</date><authorinitials>IanNimmoSmith</authorinitials></revision><revision><revnumber>3</revnumber><date>2006-10-03 10:46:32</date><authorinitials>IanNimmoSmith</authorinitials></revision><revision><revnumber>2</revnumber><date>2006-10-02 17:22:46</date><authorinitials>IanNimmoSmith</authorinitials></revision><revision><revnumber>1</revnumber><date>2006-10-02 11:05:35</date><authorinitials>IanNimmoSmith</authorinitials></revision></revhistory></articleinfo><para>Here is a typical structure for a batch script </para><orderedlist numeration="arabic"><listitem><para>{{{Code to set up parameters across all the datasets </para></listitem></orderedlist><para>and do bits of analysis that are can be grouped }}} </para><orderedlist numeration="arabic"><listitem><para>{{{Loop over Subjects and Sessions </para></listitem></orderedlist><itemizedlist><listitem override="none"><para>and perform the Main Crunch </para></listitem></itemizedlist><para>}}} </para><para>E.g. </para><orderedlist numeration="arabic"><listitem><screen><![CDATA[% reorientation, slice timing
do_time_place5
realign_spm5
smooth_spm5
]]><![CDATA[
% hp filter
MYV.hf_cut = 60;]]></screen></listitem><listitem><screen><![CDATA[% Run models
for sb = 1:length(MYV.subjects)
  for ss = 1:length(MYV.sesses)
    one_sub_sess_model_moves5(MYV, sb, ss);
    one_sub_sess_con_moves5(MYV, sb, ss);
  end
end]]></screen></listitem></orderedlist><para>Here </para><itemizedlist><listitem override="none"><para><emphasis>do_time_place<!--Warning: Probably not emitting right sort of linebreak-->
 realign_spm5<!--Warning: Probably not emitting right sort of linebreak-->
 smooth_spm5<!--Warning: Probably not emitting right sort of linebreak-->
 one_sub_sess_model_moves5</emphasis> (<ulink url="https://lsr-wiki-01.mrc-cbu.cam.ac.uk/imaging/BitOfScript/imaging/OneSubSess#">OneSubSess</ulink>)</para></listitem></itemizedlist><para>and  </para><itemizedlist><listitem override="none"><para><emphasis>one_sub_sess_con_moves5<!--Warning: Probably not emitting right sort of linebreak-->
</emphasis> </para></listitem></itemizedlist><para>are subscripts tailored to specialised parts of the sequence. </para><!--rule (<hr>) is not applicable to DocBook--></article>