<?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>WorkingOutNipy</title><revhistory><revision><revnumber>6</revnumber><date>2013-03-08 10:28:28</date><authorinitials>localhost</authorinitials><revremark>converted to 1.6 markup</revremark></revision><revision><revnumber>5</revnumber><date>2007-07-25 18:25:22</date><authorinitials>devel03.mrc-cbu.cam.ac.uk</authorinitials></revision><revision><revnumber>4</revnumber><date>2007-07-24 17:59:05</date><authorinitials>devel03.mrc-cbu.cam.ac.uk</authorinitials></revision><revision><revnumber>3</revnumber><date>2007-07-24 17:06:51</date><authorinitials>devel06.mrc-cbu.cam.ac.uk</authorinitials></revision><revision><revnumber>2</revnumber><date>2007-07-24 17:03:19</date><authorinitials>devel06.mrc-cbu.cam.ac.uk</authorinitials></revision><revision><revnumber>1</revnumber><date>2007-07-24 16:27:03</date><authorinitials>devel06.mrc-cbu.cam.ac.uk</authorinitials></revision></revhistory></articleinfo><section><title>Working out NIPY</title><para>For a web interface to the code tree: <ulink url="http://projects.scipy.org/neuroimaging/ni/browser/ni/trunk"/> </para><para>Useful examples (not quite quick start): <ulink url="http://projects.scipy.org/neuroimaging/ni/browser/ni/trunk/examples/quickstart"/> </para><para>For a basic introduction to setting up designs:  </para><itemizedlist><listitem><para><ulink url="http://projects.scipy.org/neuroimaging/ni/browser/ni/trunk/examples/quickstart/design_models.py"/> </para></listitem><listitem><para><ulink url="http://projects.scipy.org/neuroimaging/ni/browser/ni/trunk/examples/quickstart/design_regressors.py"/> </para></listitem></itemizedlist><para>To run an example script where we are, start <code>ipython --pylab</code>, then: </para><screen><![CDATA[run /home/ian/devel_trees/nipy/examples/quickstart/design_models.py]]></screen><para>(you need the ipython <code>--pylab</code> option to allow matplotlib to keep producing figures without locking the console). </para><para>The generic models code is in scipy.sandbox.models - to find where this is on the system (ipython): </para><screen><![CDATA[import scipy.sandbox.models
scipy.sandbox.models.__file__]]></screen><section><title>How to estimate a model on data</title><para>See: <ulink url="http://projects.scipy.org/scipy/scipy/browser/trunk/Lib/sandbox/models/regression.py"/> for an example, and the models directory  in general for the models code. </para><para>At interactive prompt, after running the example script above, you have a 'design' variable - which is just a design matrix: </para><screen><![CDATA[import numpy as N
import scipy.sandbox.models as SSM
]]><![CDATA[
# Make some random data
n_time_points = design.shape[1]
rY = N.random.normal(size=(n_time_points,))
]]><![CDATA[
# Estimate the model
# Note FMRI design needs transpose to standard rows = timepoints orientation
pain_glm = SSM.glm(design.T)
pain_results = pain_glm.fit(rY)]]></screen><para>See also: <ulink url="http://imaging.mrc-cbu.cam.ac.uk/svn/cbumethods/parameters/trunk/scripts/run_models.py"/> for live data example.  </para><itemizedlist><listitem><para>Example for FMRI: see <ulink url="http://projects.scipy.org/neuroimaging/ni/browser/ni/trunk/neuroimaging/modalities/fmri/fmristat/utils.py"/> </para></listitem></itemizedlist></section></section></article>