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<html><head><meta http-equiv="Content-Type" content="text/html; charset=ISO-8859-1"><title>MFBOX - Model-free processing of (fMRI) data</title><meta name="generator" content="DocBook XSL Stylesheets V1.74.0"></head><body bgcolor="white" text="black" link="#0000FF" vlink="#840084" alink="#0000FF"><div class="book" lang="en"><div class="titlepage"><div><div><h1 class="title"><a name="mfbox"></a> MFBOX - Model-free processing of (fMRI) data </h1></div><div><div class="authorgroup"><div class="author"><h3 class="author"><span class="firstname">Peter</span> <span class="surname">Gruber</span></h3></div><div class="author"><h3 class="author"><span class="firstname">Fabian</span> <span class="othername">J</span> <span class="surname">Theis</span></h3></div><div class="author"><h3 class="author"><span class="firstname">Ingo</span> <span class="othername">R</span> <span class="surname">Keck</span></h3></div></div></div></div><hr></div><div class="toc"><p><b>Table of Contents</b></p><dl><dt><span class="preface"><a href="#id2516216">Summary</a></span></dt><dt><span class="chapter"><a href="#structure">1. Structure</a></span></dt><dd><dl><dt><span class="section"><a href="#flow">Program flow</a></span></dt><dt><span class="section"><a href="#functions">Function relations</a></span></dt></dl></dd><dt><span class="chapter"><a href="#pre_algos">2. Preprocessing algorithms</a></span></dt><dd><dl><dt><span class="section"><a href="#remmeans">Removing means medians etc.</a></span></dt></dl></dd><dt><span class="chapter"><a href="#bss_algos">3. Modell-free data analysis algorithms</a></span></dt><dd><dl><dt><span class="section"><a href="#bss">Blind Source Separation (BSS)</a></span></dt><dt><span class="section"><a href="#ica">Independent Component Analysis (ICA)</a></span></dt><dt><span class="section"><a href="#pearsonica">Pearson ICA</a></span></dt><dt><span class="section"><a href="#jade">JADE</a></span></dt></dl></dd><dt><span class="chapter"><a href="#rel_algos">4. Complex component analysis and postprocessing</a></span></dt><dd><dl><dt><span class="section"><a href="#reliability">Reliability analysis with pk-means</a></span></dt><dt><span class="section"><a href="#timewindow">Sliding timewindow analysis</a></span></dt><dt><span class="section"><a href="#parametersweep">Parameter sweep</a></span></dt><dt><span class="section"><a href="#hierarchical">Hierarchical component analysis</a></span></dt></dl></dd><dt><span class="chapter"><a href="#installinstructions">5. Installation</a></span></dt><dd><dl><dt><span class="section"><a href="#spmtoolbox">Installation as SPM5 toolbox</a></span></dt><dt><span class="section"><a href="#standalone">Standalone installation</a></span></dt></dl></dd><dt><span class="reference"><a href="#function">I. Function reference</a></span></dt><dd><dl><dt><span class="refentrytitle"><a href="#spm_mf_box">Modell-free SPM plugin</a></span><span class="refpurpose"> — main window of the MFBOX</span></dt><dt><span class="refentrytitle"><a href="#mfbox_runbatch">mfbox_runbatch</a></span><span class="refpurpose"> — run analysis batch jobs</span></dt><dt><span class="refentrytitle"><a href="#mfbox_pearsonica">Pearson ICA</a></span><span class="refpurpose"> — Pearson ICA window</span></dt><dt><span class="refentrytitle"><a href="#mfbox_hNMF">Hyperplane NMF</a></span><span class="refpurpose"> — Hyperplane NMF window</span></dt><dt><span class="refentrytitle"><a href="#mfbox_hrfica">ICA with HRF constraint</a></span><span class="refpurpose"> — ICA with HRF constraint window</span></dt><dt><span class="refentrytitle"><a href="#mfbox_jade">JADE</a></span><span class="refpurpose"> — JADE window</span></dt><dt><span class="refentrytitle"><a href="#mfbox_mdsobi">Multidimensional SOBI</a></span><span class="refpurpose"> — Multidimensional SOBI window</span></dt><dt><span class="refentrytitle"><a href="#mfbox_stJADE">Spatiotemporal JADE</a></span><span class="refpurpose"> — Spatiotemporal JADE window</span></dt><dt><span class="refentrytitle"><a href="#mfbox_stSOBI">Spatiotemporal SOBI</a></span><span class="refpurpose"> — Spatiotemporal SOBI window</span></dt><dt><span class="refentrytitle"><a href="#mfbox_temporalica">Temporal Pearson ICA using PAST for dimension reduction</a></span><span class="refpurpose"> — Temporal ICA window</span></dt><dt><span class="refentrytitle"><a href="#mfbox_pre_datavalue">Mask selection by value</a></span><span class="refpurpose"> — Mask selection by value window</span></dt><dt><span class="refentrytitle"><a href="#mfbox_pre_denoise">Denoise data</a></span><span class="refpurpose"> — Denoise data window</span></dt><dt><span class="refentrytitle"><a href="#mfbox_pre_infomap">Spatiotemporal dimension adaptation</a></span><span class="refpurpose"> — Spatiotemporal dimension adaptation window</span></dt><dt><span class="refentrytitle"><a href="#mfbox_pre_remmean">Mean/trend removal</a></span><span class="refpurpose"> — Mean/trend removal window</span></dt><dt><span class="refentrytitle"><a href="#mfbox_pre_roiselect">Mask selection using brainmask</a></span><span class="refpurpose"> — Mask selection using brainmask window</span></dt><dt><span class="refentrytitle"><a href="#mfbox_pre_selectslices">Select slices for masking</a></span><span class="refpurpose"> — Select slices for masking window</span></dt><dt><span class="refentrytitle"><a href="#mfbox_pre_varthreshold">Mask selection by voxel variance</a></span><span class="refpurpose"> — Mask selection by voxel variance</span></dt><dt><span class="refentrytitle"><a href="#mfbox_rel_hierarchical">Hierarchical analysis</a></span><span class="refpurpose"> — Hierarchical analysis window</span></dt><dt><span class="refentrytitle"><a href="#mfbox_rel_none">Simple BSS analysis</a></span><span class="refpurpose"> — Simple BSS analysis window</span></dt><dt><span class="refentrytitle"><a href="#mfbox_rel_pkmeans">Reliability analysis using pk-means</a></span><span class="refpurpose"> — Reliability analysis using pk-means window</span></dt><dt><span class="refentrytitle"><a href="#mfbox_rel_window">Sliding time-window analysis</a></span><span class="refpurpose"> — Sliding time-window analysis</span></dt><dt><span class="refentrytitle"><a href="#mfbox_pos_denoise">Temporal/Spatial denoising</a></span><span class="refpurpose"> — Temporal/Spatial denoising window</span></dt><dt><span class="refentrytitle"><a href="#mfbox_pos_selectcomp">Select components</a></span><span class="refpurpose"> — Select components window</span></dt><dt><span class="refentrytitle"><a href="#mfbss">mfbss structure</a></span><span class="refpurpose"> — main structure containing all data</span></dt></dl></dd><dt><span class="chapter"><a href="#tutorials">6. Tutorials and Examples</a></span></dt><dd><dl><dt><span class="section"><a href="#toydatatutorial">Demonstration of the features of the MFBOX on the supplied toydata</a></span></dt><dt><span class="section"><a href="#spmtutorial">Analyzing the SPM demo data with MFBOX</a></span></dt><dt><span class="section"><a href="#example">Example result</a></span></dt></dl></dd><dt><span class="bibliography"><a href="#id2528934">Bibliography</a></span></dt></dl></div><div class="preface" lang="en"><div class="titlepage"><div><div><h2 class="title"><a name="id2516216"></a>Summary</h2></div></div></div><div class="highlights"><table class="simplelist" border="0" summary="Simple list"><tr><td>advanced model-free analysis of multivariate data sets</td></tr><tr><td>powerful pre- and post-processing options</td></tr><tr><td>easy to use, but flexible and extensible</td></tr><tr><td>various component and result visualization tools</td></tr><tr><td>save, load and export your results</td></tr></table></div><div class="abstract"><p class="title"><b>Abstract</b></p><p> The model-free toolbox or MFBOX for short is a simple to use Matlab toolbox for performing model-free analysis of multivariate data sets. Its main focus lies on the analysis of fMRI data sets with various model-free or data-driven techniques. So far it is closely intergrated with SPM5 and use it for im- and export and data display. </p><p> The graphical user interface of MFBOX enables users to easily try out various model-free algorithms, together with additional pre- and postprocessing algorithms and reliability analyses. The design of the toolbox is modular, so it can be easily extended to include your algorithm of choice. It plugs into SPM and can be used to perform model-free analysis of biomedical image time series such as fMRI or PET data sets, but can also be used stand-alone. </p><p> The toolbox has been developed by Peter Gruber, Ingo Keck and Fabian Theis from the Signal Processing and Information Theory group at the Institute of Biophysics, University of Regensburg, Germany. It is provided as free software subject to the GNU General Public License. Associated members of the MFBOX development-team is Elmar Lang, who greatly helped during planning, development, testing and of course funding. MFBOX is a tool to analyze fMRI data sets with various modell-free or data-driven techniques. So far it is closely intergrated with SPM5 and use it for im- and export and data display. </p></div></div><div class="chapter" lang="en"><div class="titlepage"><div><div><h2 class="title"><a name="structure"></a>Chapter⌨️ 快捷键说明
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