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<font size="5" face="Arial, Helvetica, sans-serif" color="#000099"><b>
                <br> &nbsp &nbsp
                Brain Imaging Toolbox </b></font>
<img src="images/pattern_bkgd1.gif" width="507" height="20" alt="ROI toolbox page"> 
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                Introduction </b></font></td></tr>
   
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                    The BIT (Brain Imaging Toolbox) is a graphical user interface to many handy
                    programs for artifact detection/rejection, generating ROIs, and analyzing data
                    that is in an ROI. It also contains various utility programs.
                    There are a few programs in the toolbox that were written outside of the
                    gablab and the URLs for those programs can be found below.  The utilities are
                    grouped into nine categories with a brief description of the groups and specific programs below.
                    However, you can access detailed from the links within this document, or by pressing the 
                    help button near each program button in the ROI toolbox itself.
                    If you have any questions or comments about the Toolbox's functionality or usage, please ask  
                    <a href="mailto:swg@mit.edu">Sue</a> (swg@mit.edu) or 
                    <a href="mailto:shaym@mit.edu">Shay</a> (shaym@mit.edu).
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                What's New </b></font></td> </tr>

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                        <b>
                        Release Notes (04/2007)</b></font></td></tr>

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                        <li> a new category: Connectivity Analysis, currently contains
                            just a single utility for analysis of 
                            <a href="matlab:roi_toolbox3_help('functional_connectivity_readme.txt')"> 
                            functional connectivity </a>.</li>
                        <li> the artifact detection tool now handles FSL motion data (.par files) as well as SPM .txt files. </li>
                        <li> the artifact detection tool now lets you superimpose the task conditions on one of the graphs so 
                        you can visually check for correlations with the global mean or with the motion parameters. </li>
                        <li> the global-task correlation utility was written from scratch. You can now correalte the global
                        activation mean with the task conditions and can choose whether to collapse 
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                        <b>
                        Release Notes (03/2007)</b></font></td></tr>

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                        <li> new user interface that will (hopefully) make navigation between the numerous utilities more intuitive including individual help buttons for each utility. <\li>
                        <li> you can now launch xjview and mricro directly from the toolbox. </li>
                        <li> new global and motion artifact detection tool - shows the temporal changes in both the global activation signal and motion data and enables the user to define artifacts by hand or by setting thresholds for 
                        each parameter. You can now choose to work with the temporal difference series instead of the original motion parameters values (Thanks, Dan!).</li>
                        <li> new motion-task correlation analysis tool - depending on the kind of experimental design and data format, this tool may be used to display the correlation matrix between task conditions and motion parameters, with specialized tests for block design experiments.</li>
                        <li> an easy to use interface for directly defining functional ROIs - based on an existing design matrix and contrasts files. After choosing the seed voxel the user may define the volume of interest and save the ROI to text files or to analyze images. </li>
                        <li> a utility for applying filters (low/band/high pass) to analyze (.img) files.</li>
                        <li> some minor bug fixes (timeseries, roi_deconvolve). </li>
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                Categories </b></font></td></tr>
   
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                    <td>&nbsp;</td>
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                            <a href="#artifacts"> 
                            Artifacts</a></b></font></td>
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                                These tools help you find scanner artifacts or outliers in your data caused by radical 
                                head motion or scanner mishap, and repair or remove them. To read a 
                                description of how these repairs work with the SPM analysis, press 
                                <a href="matlab:roi_toolbox3_help('artifact_protocol.txt')"> here</a>.
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                            <a href="#correlations"> <b> 
                            Correlations</b></a></font></td> 
                            
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                            Tools for analysis of motion-task and global-task correlations. </font></td> </tr>

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                            <a href="#roi_defs"> <b> 
                            ROI Definitions</b></a></font></td> 
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                            Tools to generate and manipulate anatomical and functional based regions of interest. </font></td> </tr>

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                            <a href="#roi_analysis"> <b> 
                            ROI Analysis</b></a></font></td> 
                            <td><font face="Arial, Helvetica, sans-serif" size="3"> 
                                These tools extract statistics, time course histories and measures of activation 
                                within a region of interest  over an entire timecourse of images.
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                            <a href="#connectivity_analysis"> <b> 
                            Connectivity Analysis</b></a></font></td> 
                            <td><font face="Arial, Helvetica, sans-serif" size="3"> 
                                Tools (currently a single tool) for analysis of connectivity between 
                                regions of interest.
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                            <a href="#display"> <b> 
                            Display</b></a></font></td> 
                            <td><font face="Arial, Helvetica, sans-serif" size="3"> 
                                These tools provide several different ways to visualize your region of 
                                interest in an interactive fashion or in one suitable for printing.
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                            <a href="#tal"> <b> 
                            Talairach Atlas</b></a></font></td>
                            <td><font face="Arial, Helvetica, sans-serif" size="3"> 
                                These programs allow direct use of the Talairach Atlas (instead of WFU_PickAtlas).                  
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                            <a href="#general"> <b> 
                            General Utilities</b></a></font></td>
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                                These programs are automated tools for common user functions
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                            <a href="#coord"> <b> 
                            Coordinate Conversions</b></a></font></td>
                            <td><font face="Arial, Helvetica, sans-serif" size="3"> 
                                The tools in this section work together to allow conversions between different representation of ROIs.
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                    <a id="artifacts">Artifacts</a></b></font></td>
 
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                        <!--<a href="matlab:roi_toolbox3_help('art_readme.txt')"> <b> -->
                        <a href="art.html"> <b>
                        Global and Motion Outliers</b></a></font></td> 
                        <td><font face="Arial, Helvetica, sans-serif" size="3"> 
shows the temporal changes in both the global activation signal and motion data and enables the user to define artifacts by hand or by setting thresholds for each parameter.
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                        <a href="matlab:roi_toolbox3_help('spike_repair_readme.txt')"> <b>
                        Slice Repair</b></a></font></td> 
                        <td><font face="Arial, Helvetica, sans-serif" size="3"> 
                        Checks for outlier slices, and offers repair methods.
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                        <a href="matlab:roi_toolbox3_help('constrast_movie_readme.txt')"> <b>
                        Contrast Movie</b></a></font></td> 
                        <td><font face="Arial, Helvetica, sans-serif" size="3"> 
                        Allows a user to view all the data, voxel by voxel.
                        </font></td> </tr>
 
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                        <a href="matlab:roi_toolbox3_help('global_variate_readme.txt')"> <b>
                        Global Variate</b></a></font></td> 
                        <td><font face="Arial, Helvetica, sans-serif" size="3"> 
                        Old version of the artifacts detection utility. Contains some repair functionality that the new version does not, but only handles global activation outliers.
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                        <a href="matlab:roi_toolbox3_help('globalmask_readme.txt')"> <b>
                        GlmMask2</b></a></font></td> 
                        <td><font face="Arial, Helvetica, sans-serif" size="3"> 
                        bypasses spm_global routine that generates the mask.img and lets the user explicitly define a mask to get full brain coverage in 1st level satistics.
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                        <a href="matlab:roi_toolbox3_help('apply_filter_readme.txt')"> <b>
                        Apply Filter</b></a></font></td> 
                        <td><font face="Arial, Helvetica, sans-serif" size="3"> 
                        applies a low/band/high-pass filter to a series of analyze .img files
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                    <a id="correlations">Correlations</a></b></font></td>
 
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                        <td height="18"><font face="Arial, Helvetica, sans-serif" size="3"> 
 
                        <a href="matlab:roi_toolbox3_help('taskcorr.txt')"> <b>
                        Motion-Task Correlations</b></a></font></td> 
                        <td><font face="Arial, Helvetica, sans-serif" size="3"> 
displays the correlation matrix between task conditions and motion parameters. Implements specialized tests for block design experiments.
                        </font></td> </tr>
 
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                            <td>&nbsp;</td>
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                        <td><div align="center"><img src="images/bullet_orange.gif" alt="bullet" width="6" height="6"><font face="Arial, Helvetica, sans-serif" size="2"><b></b></font></div></td>
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                        <a href="matlab:roi_toolbox3_help('sm_gltaskcorr_readme.txt')"> <b>
                        Global-Task Correlation</b></a></font></td> 
                        <td><font face="Arial, Helvetica, sans-serif" size="3"> 
                        displays correlations between the global mean activation and the task conditions.
                        </font></td> </tr>
 
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                </tr>
                <tr> 
                    <td height="5"><img src="images/pixelclear.gif" width="1" height="1"></td>
                    <td height="5"><img src="images/pixelclear.gif" width="1" height="1"></td>
                </tr>
                <tr> 
                    <td><div style="margin-left:5px;"></div></td>
                    <td><font size="4" face="Arial, Helvetica, sans-serif" color="#000099"><b> 

                    <a id="roi_defs">ROI Definitions</a></b></font></td>
 
                </tr>
                <tr> 
                    <td height="10"><img src="images/pixelclear.gif" width="1" height="1"></td>
                    <td>&nbsp;</td>
                </tr>
            </table>
            <table width="95%" border="0" cellspacing="0" cellpadding="0">
                                    
                <tr> 
                    <td width="15"><img src="images/pixelclear.gif" width="15" height="15"></td>
                    <td> <table width="100%" border="0" cellspacing="0" cellpadding="0">
                    

                    <tr> 
                        <td> <div align="center"><img src="images/bullet_orange.gif" alt="bullet" width="6" height="6"><font face="Arial, Helvetica, sans-serif" size="2"><b></b></font></div></td>
                        <td height="18"><font face="Arial, Helvetica, sans-serif" size="3"> 
 
                        <a href="matlab:roi_toolbox3_help('mni_or_tal_rois_readme.txt')"> <b>
                        Anatomical ROIs</b></a></font></td> 
                        
                        <td><font face="Arial, Helvetica, sans-serif" size="3"> 
Utility to create ROI coordinate sets (.tal files) from anatomical/Brodmann landmarks.
                        </font></td> </tr>
 
                        <tr> 
                            <td height="10"> <div align="center"></div></td>
                            <td>&nbsp;</td>
                        </tr>

                        <tr> 
                        <td><div align="center"><img src="images/bullet_orange.gif" alt="bullet" width="6" height="6"><font face="Arial, Helvetica, sans-serif" size="2"><b></b></font></div></td>
                        <td height="18"><font face="Arial, Helvetica, sans-serif" size="3"> 
 
                        <a href="matlab:roi_toolbox3_help('functionalROI_readme.txt')"> <b>
                        Functional ROIs</b></a></font></td> 
                        <td><font face="Arial, Helvetica, sans-serif" size="3"> 
                        Creates a .tal and .img ROI file based on specified XYZ dimensions in voxels.
                        </font></td> </tr>
 
                        <tr> 
                            <td height="10"> <div align="center"></div></td>
                            <td>&nbsp;</td>
                        </tr>

                    </table>

                    </td>
                </tr>
                
                
            </table>

            <!-- END ROI defs SECTION -->

            <!-- BEGIN ROI analysis SECTION -->

            <table width="95%" border="0" cellspacing="0" cellpadding="0">
                <tr> 
                    <td width="5" height="1"><img src="images/pixelclear.gif" width="1" height="1"></td>
                    <td height="1" bgcolor="#003366"><img src="images/pixelclear.gif" width="1" height="1"></td>
                </tr>
                <tr> 
                    <td height="5"><img src="images/pixelclear.gif" width="1" height="1"></td>
                    <td height="5"><img src="images/pixelclear.gif" width="1" height="1"></td>
                </tr>
                <tr> 
                    <td><div style="margin-left:5px;"></div></td>
                    <td><font size="4" face="Arial, Helvetica, sans-serif" color="#000099"><b> 

                    <a id="roi_analysis">ROI Analysis</a></b></font></td>
 
                </tr>
                <tr> 
                    <td height="10"><img src="images/pixelclear.gif" width="1" height="1"></td>
                    <td>&nbsp;</td>
                </tr>
            </table>
            <table width="95%" border="0" cellspacing="0" cellpadding="0">
                                    
                <tr> 
                    <td width="15"><img src="images/pixelclear.gif" width="15" height="15"></td>
                    <td> <table width="100%" border="0" cellspacing="0" cellpadding="0">
                    

                    <tr> 
                        <td> <div align="center"><img src="images/bullet_orange.gif" alt="bullet" width="6" height="6"><font face="Arial, Helvetica, sans-serif" size="2"><b></b></font></div></td>
                        <td height="18"><font face="Arial, Helvetica, sans-serif" size="3"> 
 
                        <a href="matlab:roi_toolbox3_help('roi_stats_readme.txt')"> <b>
                        ROI stats</b></a></font></td> 
                        <td><font face="Arial, Helvetica, sans-serif" size="3"> 
 finds mean, min, max, and variance of data in an ROI for each image in a series.
  ROI is defined by a .img file.                       
                        </font></td> </tr>
 
                        <tr> 
                            <td height="10"> <div align="center"></div></td>
                            <td>&nbsp;</td>
                        </tr>

                        <tr> 
                        <td><div align="center"><img src="images/bullet_orange.gif" alt="bullet" width="6" height="6"><font face="Arial, Helvetica, sans-serif" size="2"><b></b></font></div></td>
                        <td height="18"><font face="Arial, Helvetica, sans-serif" size="3"> 
 
                        <a href="matlab:roi_toolbox3_help('roi_extract_readme.txt')"> <b>
                        ROI extract</b></a></font></td> 
                        <td><font face="Arial, Helvetica, sans-serif" size="3"> 
finds the mean intensity of an ROI for each user specified image. ROI
  is a .tal list of coordinates.
                        
                        </font></td> </tr>
 
                        <tr> 
                            <td height="10"> <div align="center"></div></td>
                            <td>&nbsp;</td>
                        </tr>

                        <tr> 
                        <td> <div align="center"><img src="images/bullet_orange.gif" alt="bullet" width="6" height="6"><font face="Arial, Helvetica, sans-serif" size="2"><b></b></font></div></td>
                        <td height="18"><font face="Arial, Helvetica, sans-serif" size="3"> 
 
                        <a href="matlab:roi_toolbox3_help('percent_signal_change_readme.txt')"> <b>
                        X-Beta</b></a></font></td> 
                        <td><font face="Arial, Helvetica, sans-serif" size="3"> 
                        a utility program to run roi_stats on multiple beta files. A good program 
  to correlate fMRI data with behavioral data.
                        </font></td> </tr>
 
                        <tr> 
                            <td height="10"> <div align="center"></div></td>
                            <td>&nbsp;</td>
                        </tr>
 
                        <tr> 
                        <td> <div align="center"><img src="images/bullet_orange.gif" alt="bullet" width="6" height="6"><font face="Arial, Helvetica, sans-serif" size="2"><b></b></font></div></td>
                        <td height="18"><font face="Arial, Helvetica, sans-serif" size="3"> 
 
                        <a href="matlab:roi_toolbox3_help('timeseries_explorer_readme.txt')"> <b>
                        Timeseries Explorer</b></a></font></td> 
                        <td><font face="Arial, Helvetica, sans-serif" size="3"> 
an interactive display of timecourses from single voxels or ROIs. It also
  provides signal processing options and displays percent signal change for all specified conditions.
                        </font></td> </tr>
 
                        <tr> 
                            <td height="10"> <div align="center"></div></td>
                            <td>&nbsp;</td>
                        </tr>

                        <tr> 
                        <td> <div align="center"><img src="images/bullet_orange.gif" alt="bullet" width="6" height="6"><font face="Arial, Helvetica, sans-serif" size="2"><b></b></font></div></td>
                        <td height="18"><font face="Arial, Helvetica, sans-serif" size="3"> 
 
                        <a href="matlab:roi_toolbox3_help('roi_HRFestimate_readme.txt')"<b>
                        ROI HRF Estimate</b></a></font></td> 
                        <td><font face="Arial, Helvetica, sans-serif" size="3"> 
estimates the HRF responses to different conditions within an ROI.
                        </font></td> </tr>
 
                        <tr> 
                            <td height="10"> <div align="center"></div></td>
                            <td>&nbsp;</td>
                        </tr>
                    </table>

                    </td>
                </tr>
                
                
            </table>

            <!-- END ROI analysis SECTION -->

            <!-- BEGIN Connectivity Analysis SECTION -->

            <table width="95%" border="0" cellspacing="0" cellpadding="0">
                <tr> 
                    <td width="5" height="1"><img src="images/pixelclear.gif" width="1" height="1"></td>
                    <td height="1" bgcolor="#003366"><img src="images/pixelclear.gif" width="1" height="1"></td>
                </tr>
                <tr> 
                    <td height="5"><img src="images/pixelclear.gif" width="1" height="1"></td>
                    <td height="5"><img src="images/pixelclear.gif" width="1" height="1"></td>
                </tr>
                <tr> 
                    <td><div style="margin-left:5px;"></div></td>
                    <td><font size="4" face="Arial, Helvetica, sans-serif" color="#000099"><b> 

                    <a id="connectivity_analysis">Connectivity Analysis</a></b></font></td>
 
                </tr>
                <tr> 
                    <td height="10"><img src="images/pixelclear.gif" width="1" height="1"></td>
                    <td>&nbsp;</td>
                </tr>
            </table>
            <table width="95%" border="0" cellspacing="0" cellpadding="0">
                                    
                <tr> 
                    <td width="15"><img src="images/pixelclear.gif" width="15" height="15"></td>
                    <td> <table width="100%" border="0" cellspacing="0" cellpadding="0">
                    

                    <tr> 
                        <td> <div align="center"><img src="images/bullet_orange.gif" alt="bullet" width="6" height="6"><font face="Arial, Helvetica, sans-serif" size="2"><b></b></font></div></td>
                        <td height="18"><font face="Arial, Helvetica, sans-serif" size="3"> 
 
                        <a href="matlab:roi_toolbox3_help('functional_connectivity_readme.txt')"> <b>
                        Functional Connectivity</b></a></font></td> 
                        
                        <td><font face="Arial, Helvetica, sans-serif" size="3"> 
                        Utility for calculating the correlation between a source ROI and a set 
                        of target ROIs.
                        </font></td> </tr>
 
                        <tr> 
                            <td height="10"> <div align="center"></div></td>
                            <td>&nbsp;</td>
                        </tr>

                    </table>

                    </td>
                </tr>
                
                
            </table>

            <!-- END Connectivity Analysis SECTION -->

            <!-- BEGIN display SECTION -->

            <table width="95%" border="0" cellspacing="0" cellpadding="0">
                <tr> 
                    <td width="5" height="1"><img src="images/pixelclear.gif" width="1" height="1"></td>
                    <td height="1" bgcolor="#003366"><img src="images/pixelclear.gif" width="1" height="1"></td>
                </tr>
                <tr> 
                    <td height="5"><img src="images/pixelclear.gif" width="1" height="1"></td>
                    <td height="5"><img src="images/pixelclear.gif" width="1" height="1"></td>
                </tr>
                <tr> 
                    <td><div style="margin-left:5px;"></div></td>
                    <td><font size="4" face="Arial, Helvetica, sans-serif" color="#000099"><b> 

                    <a id="display">Display</a></b></font></td>
 
                </tr>
                <tr> 
                    <td height="10"><img src="images/pixelclear.gif" width="1" height="1"></td>
                    <td>&nbsp;</td>
                </tr>
            </table>
            <table width="95%" border="0" cellspacing="0" cellpadding="0">
                                    
                <tr> 
                    <td width="15"><img src="images/pixelclear.gif" width="15" height="15"></td>
                    <td> <table width="100%" border="0" cellspacing="0" cellpadding="0">
                    

                    <tr> 
                        <td> <div align="center"><img src="images/bullet_orange.gif" alt="bullet" width="6" height="6"><font face="Arial, Helvetica, sans-serif" size="2"><b></b></font></div></td>
                        <td height="18"><font face="Arial, Helvetica, sans-serif" size="3"> 
 
                        <a href="matlab:roi_toolbox3_help('display_rois_readme.txt')"> <b>
                        Display ROIs</b></a></font></td> 
                        <td><font face="Arial, Helvetica, sans-serif" size="3"> 
shows one or more ROIs in 3D interactive overlayed on a background image.
                        </font></td> </tr>
 
                        <tr> 
                            <td height="10"> <div align="center"></div></td>
                            <td>&nbsp;</td>
                        </tr>

                        <tr> 
                        <td><div align="center"><img src="images/bullet_orange.gif" alt="bullet" width="6" height="6"><font face="Arial, Helvetica, sans-serif" size="2"><b></b></font></div></td>
                        <td height="18"><font face="Arial, Helvetica, sans-serif" size="3"> 
 
                        <a href="matlab:web('http://www.mrc-cbu.cam.ac.uk/Imaging/Common/display_slices.shtml')"> <b>
                        Display Slices</b></a></font></td> 
                        <td><font face="Arial, Helvetica, sans-serif" size="3"> 
shows the same thing as a montage of slices. 
  Author: Mathew Brett. <a href="matlab:web('http://www.mrc-cbu.cam.ac.uk/Imaging/Common/display_slices.shtml')"> website </a>
                        </font></td> </tr>
 
                        <tr> 
                            <td height="10"> <div align="center"></div></td>
                            <td>&nbsp;</td>
                        </tr>

                        <tr> 
                        <td> <div align="center"><img src="images/bullet_orange.gif" alt="bullet" width="6" height="6"><font face="Arial, Helvetica, sans-serif" size="2"><b></b></font></div></td>
                        <td height="18"><font face="Arial, Helvetica, sans-serif" size="3"> 
 
                        <a href="matlab:web('http://www.neuro.lf1.cuni.cz/spm/spm_xbrain_3d.html')"> <b>
                        Render</b></a></font></td> 
                        <td><font face="Arial, Helvetica, sans-serif" size="3"> 
                        Improved version of the Render->Xtract Brain function, which allows user to create render*_.mat file containing any number of general 3D views of general cuts of the extracted brain.
  Author: Tom Sieger. <a href="matlab:web('http://www.neuro.lf1.cuni.cz/spm/spm_xbrain_3d.html')"> website </a>
                        </font></td> </tr>
 
                        <tr> 
                            <td height="10"> <div align="center"></div></td>
                            <td>&nbsp;</td>
                        </tr>
 
                        <tr> 
                        <td> <div align="center"><img src="images/bullet_orange.gif" alt="bullet" width="6" height="6"><font face="Arial, Helvetica, sans-serif" size="2"><b></b></font></div></td>
                        <td height="18"><font face="Arial, Helvetica, sans-serif" size="3"> 
 
                        <a href="matlab:roi_toolbox3_help('help_studyplot.txt')"> <b>
                        Studyplot</b></a></font></td> 
                        <td><font face="Arial, Helvetica, sans-serif" size="3"> 
                        A visualization tool for meta-analyses.
It enables the user to supply a database of activation
points, with coordinates and other information like
coordinate system, color, etc., and then have those points plotted and
labeled on a variety of different brain displays.
                        </font></td> </tr>
 
                        <tr> 
                            <td height="10"> <div align="center"></div></td>
                            <td>&nbsp;</td>
                        </tr>

                        <tr> 
                        <td> <div align="center"><img src="images/bullet_orange.gif" alt="bullet" width="6" height="6"><font face="Arial, Helvetica, sans-serif" size="2"><b></b></font></div></td>
                        <td height="18"><font face="Arial, Helvetica, sans-serif" size="3"> 
 
                        <a href="matlab:web('http://people.hnl.bcm.tmc.edu/cuixu/xjView')">  <b>
                        xjview</b></a></font></td> 
                        <td><font face="Arial, Helvetica, sans-serif" size="3"> 
                        The xjview visualization utility. Author: Xu Cui. <a href="matlab:web('http://people.hnl.bcm.tmc.edu/cuixu/xjView')"> website </a>
                        </font></td> </tr>
 
                        <tr> 
                            <td height="10"> <div align="center"></div></td>
                            <td>&nbsp;</td>
                        </tr>

                        <tr> 
                        <td> <div align="center"><img src="images/bullet_orange.gif" alt="bullet" width="6" height="6"><font face="Arial, Helvetica, sans-serif" size="2"><b></b></font></div></td>
                        <td height="18"><font face="Arial, Helvetica, sans-serif" size="3"> 
 
                        <a href="matlab:web('http://www.sph.sc.edu/comd/rorden/mricro.html')">  <b>
                        mricro</b></a></font></td> 
                        <td><font face="Arial, Helvetica, sans-serif" size="3"> 
                        The mricro utility for displaying and manipulating MRI images. Author: Chris Rorden. <a href="matlab:web('http://www.sph.sc.edu/comd/rorden/mricro.html')"> website </a>
                        </font></td> </tr>
 
                        <tr> 
                            <td height="10"> <div align="center"></div></td>
                            <td>&nbsp;</td>
                        </tr>
                    
                    </table>

                    </td>
                </tr>
                
                
            </table>

            <!-- END Display SECTION -->

            <!-- BEGIN Atlas SECTION -->

            <table width="95%" border="0" cellspacing="0" cellpadding="0">
                <tr> 
                    <td width="5" height="1"><img src="images/pixelclear.gif" width="1" height="1"></td>
                    <td height="1" bgcolor="#003366"><img src="images/pixelclear.gif" width="1" height="1"></td>
                </tr>
                <tr> 
                    <td height="5"><img src="images/pixelclear.gif" width="1" height="1"></td>
                    <td height="5"><img src="images/pixelclear.gif" width="1" height="1"></td>
                </tr>
                <tr> 
                    <td><div style="margin-left:5px;"></div></td>
                    <td><font size="4" face="Arial, Helvetica, sans-serif" color="#000099"><b> 

                    <a id="tal">Talairach Atlas</a></b></font></td>
 
                </tr>
                <tr> 
                    <td height="10"><img src="images/pixelclear.gif" width="1" height="1"></td>
                    <td>&nbsp;</td>
                </tr>
            </table>
            <table width="95%" border="0" cellspacing="0" cellpadding="0">
                                    
                <tr> 
                    <td width="15"><img src="images/pixelclear.gif" width="15" height="15"></td>
                    <td> <table width="100%" border="0" cellspacing="0" cellpadding="0">
                    

                    <tr> 
                        <td> <div align="center"><img src="images/bullet_orange.gif" alt="bullet" width="6" height="6"><font face="Arial, Helvetica, sans-serif" size="2"><b></b></font></div></td>
                        <td height="18"><font face="Arial, Helvetica, sans-serif" size="3"> 
 
                        <a href="matlab:roi_toolbox3_help('display_talspace_readme.txt')"> <b>
                        Display_TalSpace</b></a></font></td> 
                        <td><font face="Arial, Helvetica, sans-serif" size="3"> 
Displays functional clusters on Talairach atlas pages, and renders them in 3-D.
                        </font></td> </tr>
 
                        <tr> 
                            <td height="10"> <div align="center"></div></td>
                            <td>&nbsp;</td>
                        </tr>

                        <tr> 
                        <td><div align="center"><img src="images/bullet_orange.gif" alt="bullet" width="6" height="6"><font face="Arial, Helvetica, sans-serif" size="2"><b></b></font></div></td>
                        <td height="18"><font face="Arial, Helvetica, sans-serif" size="3"> 
 
                        <a href="matlab:roi_toolbox3_help('spm_tal_stats_readme.txt')"> <b>
                        Dump SPM to Tal</b></a></font></td> 
                        <td><font face="Arial, Helvetica, sans-serif" size="3"> 
(glassbrain2.m) creates a list of points in Talairach space from
  a cluster region in SPM. Like Dump SPM to Anatomy, but this one returns only the Tal
  coordinates, suitable for input to the Talairach Daemon.
                        </font></td> </tr>
 
                        <tr> 
                            <td height="10"> <div align="center"></div></td>
                            <td>&nbsp;</td>
                        </tr>

                        <tr> 
                        <td> <div align="center"><img src="images/bullet_orange.gif" alt="bullet" width="6" height="6"><font face="Arial, Helvetica, sans-serif" size="2"><b></b></font></div></td>
                        <td height="18"><font face="Arial, Helvetica, sans-serif" size="3"> 
 
                        <a href="matlab:roi_toolbox3_help('na_readme.txt')"> <b>
                        Tal stats summary</b></a></font></td> 
                        <td><font face="Arial, Helvetica, sans-serif" size="3"> 
(sum_coord.m) summarizes an output file generated by the Talairach 
  Daemon program.
                        </font></td> </tr>
 
                        <tr> 
                            <td height="10"> <div align="center"></div></td>
                            <td>&nbsp;</td>
                        </tr>
                    </table>

                    </td>
                </tr>
                
                
            </table>

            <!-- END Atlas SECTION -->

            <!-- BEGIN general utilities SECTION -->

            <table width="95%" border="0" cellspacing="0" cellpadding="0">
                <tr> 
                    <td width="5" height="1"><img src="images/pixelclear.gif" width="1" height="1"></td>
                    <td height="1" bgcolor="#003366"><img src="images/pixelclear.gif" width="1" height="1"></td>
                </tr>
                <tr> 
                    <td height="5"><img src="images/pixelclear.gif" width="1" height="1"></td>
                    <td height="5"><img src="images/pixelclear.gif" width="1" height="1"></td>
                </tr>
                <tr> 
                    <td><div style="margin-left:5px;"></div></td>
                    <td><font size="4" face="Arial, Helvetica, sans-serif" color="#000099"><b> 

                    <a id="general">General Utilities</a></b></font></td>
 
                </tr>
                <tr> 
                    <td height="10"><img src="images/pixelclear.gif" width="1" height="1"></td>
                    <td>&nbsp;</td>
                </tr>
            </table>
            <table width="95%" border="0" cellspacing="0" cellpadding="0">
                                    
                <tr> 
                    <td width="15"><img src="images/pixelclear.gif" width="15" height="15"></td>
                    <td> <table width="100%" border="0" cellspacing="0" cellpadding="0">
                    

                    <tr> 
                        <td> <div align="center"><img src="images/bullet_orange.gif" alt="bullet" width="6" height="6"><font face="Arial, Helvetica, sans-serif" size="2"><b></b></font></div></td>
                        <td height="18"><font face="Arial, Helvetica, sans-serif" size="3"> 
 
                        <a href="matlab:roi_toolbox3_help('glassbrain32_readme.txt')"> <b>
                        DumpSPM to Anatomy</b></a></font></td> 
                        <td><font face="Arial, Helvetica, sans-serif" size="3"> 
dumps voxels from SPM Results/Volumes table, and names all the points.
   Allows the user to identify anatomy locations of active SPM cluster regions.
                        </font></td> </tr>
 
                        <tr> 
                            <td height="10"> <div align="center"></div></td>
                            <td>&nbsp;</td>
                        </tr>

                        <tr> 
                        <td><div align="center"><img src="images/bullet_orange.gif" alt="bullet" width="6" height="6"><font face="Arial, Helvetica, sans-serif" size="2"><b></b></font></div></td>
                        <td height="18"><font face="Arial, Helvetica, sans-serif" size="3"> 
 
                        <a href="matlab:roi_toolbox3_help('spm_findGM_readme.txt')"> <b>
                        Find anatomy names</b></a></font></td> 
                        <td><font face="Arial, Helvetica, sans-serif" size="3"> 
finds names  (hemisphere, lobe, Brodmann area)  for one or more 
   [XYZ] points in MNI space using the WFU_PickAtlas database.
                        </font></td> </tr>
 
                        <tr> 
                            <td height="10"> <div align="center"></div></td>
                            <td>&nbsp;</td>
                        </tr>

                        <tr> 
                        <td> <div align="center"><img src="images/bullet_orange.gif" alt="bullet" width="6" height="6"><font face="Arial, Helvetica, sans-serif" size="2"><b></b></font></div></td>
                        <td height="18"><font face="Arial, Helvetica, sans-serif" size="3"> 
 
                        <a href="matlab:roi_toolbox3_help('badpathname_readme.txt')"> <b>
                        Modify Pathnames</b></a></font></td> 
                        <td><font face="Arial, Helvetica, sans-serif" size="3"> 
When files are moved or old files are restored, the names embedded
   in SPM.mat are not valid. This program (modifySPM2.m) can repair the file names.
                        </font></td> </tr>
 
                        <tr> 
                            <td height="10"> <div align="center"></div></td>
                            <td>&nbsp;</td>
                        </tr>
 
                        <tr> 
                        <td> <div align="center"><img src="images/bullet_orange.gif" alt="bullet" width="6" height="6"><font face="Arial, Helvetica, sans-serif" size="2"><b></b></font></div></td>
                        <td height="18"><font face="Arial, Helvetica, sans-serif" size="3"> 
 
                        <a href="matlab:roi_toolbox3_help('contrastcopier_readme.txt')"> <b>
                        Contrast Copier</b></a></font></td> 
                        <td><font face="Arial, Helvetica, sans-serif" size="3"> 
collects contrast images from different subjects and puts them in
   a single folder. A convenient program for 2nd analyses, eg to correlate fMRI data with behavioral data.
                        </font></td> </tr>
 
                        <tr> 
                            <td height="10"> <div align="center"></div></td>
                            <td>&nbsp;</td>
                        </tr>

                        <tr> 
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                        <td height="18"><font face="Arial, Helvetica, sans-serif" size="3"> 
 
                        <a href="matlab:roi_toolbox3_help('automask_readme.txt')"> <b>
                        Create Head Mask</b></a></font></td> 
                        <td><font face="Arial, Helvetica, sans-serif" size="3"> 
 automatically generates a reasonable full-head mask. Designed to 
   eliminate the wrap-around artifact in spiral scan data.
                        </font></td> </tr>
 
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                            <td>&nbsp;</td>
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                    </table>

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                    <td><font size="4" face="Arial, Helvetica, sans-serif" color="#000099"><b> 

                    <a id="coord">Coordinate Conversions</a></b></font></td>


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                    <td>&nbsp;</td>
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                        <tr> 
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 An ROI can be expressed as:
<li> An image of 1's and 0's. ( .img file ) </li>
<li> A list of points in MNI space  ( .txt file ) in mm units. </li>
<li> A list of points in Talaraich space ( .tal file ) in mm units. </li>
<li> A list of points in single subject space. </li>
The tools in this section work together to allow conversions between these spaces.

                        </tr>

                    <tr> 
                        <td> <div align="center"><img src="images/bullet_orange.gif" alt="bullet" width="6" height="6"><font face="Arial, Helvetica, sans-serif" size="2"><b></b></font></div></td>
                        <td height="18"><font face="Arial, Helvetica, sans-serif" size="3"> 
 
                        <a href="matlab:roi_toolbox3_help('img2txt_readme.txt')"> <b>
                        img2txt</b></a></font></td> 
                        <td><font face="Arial, Helvetica, sans-serif" size="3"> 
converts an ROI img ( in MNI space ) into list of points (.txt file.)

                        </font></td> </tr>
 
                        <tr> 
                            <td height="10"> <div align="center"></div></td>
                            <td>&nbsp;</td>
                        </tr>

                        <tr> 
                        <td><div align="center"><img src="images/bullet_orange.gif" alt="bullet" width="6" height="6"><font face="Arial, Helvetica, sans-serif" size="2"><b></b></font></div></td>
                        <td height="18"><font face="Arial, Helvetica, sans-serif" size="3"> 
 
                        <a href="matlab:roi_toolbox3_help('mni2tal_readme.txt')"> <b>
                        mni2tal</b></a></font></td> 
                        <td><font face="Arial, Helvetica, sans-serif" size="3"> 
converts a list of points in MNI space to a list in Talaraich space (.tal file). Uses Mathew Brett's conversion.

                        </font></td> </tr>
 
                        <tr> 
                            <td height="10"> <div align="center"></div></td>
                            <td>&nbsp;</td>
                        </tr>

                        <tr> 
                        <td> <div align="center"><img src="images/bullet_orange.gif" alt="bullet" width="6" height="6"><font face="Arial, Helvetica, sans-serif" size="2"><b></b></font></div></td>
                        <td height="18"><font face="Arial, Helvetica, sans-serif" size="3"> 
 
                        <a href="matlab:roi_toolbox3_help('txt2img_readme.txt')"> <b>
                        txt2img</b></a></font></td> 
                        <td><font face="Arial, Helvetica, sans-serif" size="3"> 
converts a list of points in MNI space into a .img file. Program asks for
  a sample image in order to set the voxel size and image dimensions.

                        </font></td> </tr>
 
                        <tr> 
                            <td height="10"> <div align="center"></div></td>
                            <td>&nbsp;</td>
                        </tr>
 
                        <tr> 
                        <td> <div align="center"><img src="images/bullet_orange.gif" alt="bullet" width="6" height="6"><font face="Arial, Helvetica, sans-serif" size="2"><b></b></font></div></td>
                        <td height="18"><font face="Arial, Helvetica, sans-serif" size="3"> 
 
                        <a href="matlab:roi_toolbox3_help('tal2mni_readme.txt')"> <b>
                        tal2mni</b></a></font></td> 
                        <td><font face="Arial, Helvetica, sans-serif" size="3"> 
 converts a list of points in Talaraich space to a list in MNI space. It
  appends _mni to the filename in its translation process. Uses Mathew Brett's conversion.

                        </font></td> </tr>
 
                        <tr> 
                            <td height="10"> <div align="center"></div></td>
                            <td>&nbsp;</td>
                        </tr>

                        <tr> 
                        <td> <div align="center"><img src="images/bullet_orange.gif" alt="bullet" width="6" height="6"><font face="Arial, Helvetica, sans-serif" size="2"><b></b></font></div></td>
                        <td height="18"><font face="Arial, Helvetica, sans-serif" size="3"> 
 
                        <a href="matlab:roi_toolbox3_help('reverse_norm_readme.txt')"> <b>
                        MNI to Subject</b></a></font></td> 
                        <td><font face="Arial, Helvetica, sans-serif" size="3"> 
  converts a list of points in MNI space to a list of points in
  single subject space by performing a reverse noramlization with the (_sn.mat) calculated by SPM.
                        </font></td> </tr>
 
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                            <td height="10"> <div align="center"></div></td>
                            <td>&nbsp;</td>
                        </tr>
                    </table>

                    </td>
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