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metaanalysis_ale_tutorial.html
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<!DOCTYPE HTML>
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<title>Conducting an ALE Meta-Analysis</title>
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<h1>Conducting an ALE Meta-Analysis</h1>
<h2>1. Installation of GingerALE</h2>
<p>Go to <a href="http://brainmap.org">BrainMap</a> to download the version of GingerALE for the operating system of the computer as a ZIP file.</p>
<p>Decompress the ZIP file. To avoid problems, decompress it within a local folder without blank spaces in its path.</p>
<p>Click the file GingerALE to execute the graphical interface of GingerALE.</p>
<h2>2. Preparing Data for Meta-Analysis</h2>
<h3>Foci Formatting:</h3>
<ul>
<li>Create a text file with three columns for x, y, and z coordinates, separated by tabs or spaces.</li>
<li>Optionally, start the file with a line indicating the standard brain space (Talairach or MNI).</li>
<li>Separate foci groups with a line break, including identifying information such as the first author’s name, year, experiment name, or subject group name.</li>
<li>Include the number of subjects for each group and the coordinate data. Comments should start with "//".</li>
</ul>
<img src="images/Foci_ALE_meta-analysis.png" style="width: 15%;">
<h2>3. Single Dataset Analysis</h2>
<h3>Loading Foci Data:</h3>
<ul>
<li>Open GingerALE and load your foci data using File > Open Foci.</li>
<li>GingerALE will read and verify the dataset, checking for mismatched reference spaces, missing subject sizes, and duplicated foci groups.</li>
<li>Review any errors or warnings displayed.</li>
</ul>
<h3>Performing ALE Analysis:</h3>
<ul>
<li>Once the data is loaded, choose threshold settings and begin the calculations.</li>
<li>The ALE meta-analysis follows four main steps: ALE scores, null distribution, thresholding, and cluster statistics.</li>
</ul>
<h2>4. Contrast Analyses</h2>
<h3>Running Separate ALE Analyses:</h3>
<ul>
<li>Perform separate ALE analyses on the two sets of foci.</li>
<li>Create a combined text file with foci from both files and run a pooled analysis. Ensure experiments appearing in both sets are only reported once.</li>
</ul>
<h3>Subtraction Analysis:</h3>
<ul>
<li>Select the “Contrast Studies” radio button in the main GingerALE window.</li>
<li>Open the three thresholded ALE images using the file menu items.</li>
<li>Verify settings for threshold method, number of permutations, and output file names, then click Compute.</li>
</ul>
<h2>5. Output Files</h2>
<h3>Types of Output Files:</h3>
<ul>
<li><strong>ALE Image:</strong> Contains unthresholded ALE values for every voxel in the brain.</li>
<li><strong>P Value Image:</strong> Contains unthresholded P values for each voxel.</li>
<li><strong>Thresholded Image:</strong> ALE map thresholded at a given value, used as input for contrast analyses.</li>
<li><strong>Cluster Image:</strong> Identifies contiguous non-zero regions in the thresholded image.</li>
<li><strong>Cluster Spreadsheet:</strong> Provides detailed information about the resultant clusters, including volume, coordinates, and anatomical labels.</li>
<li><strong>Data History:</strong> Contains parameters and output file names used in the analysis, along with additional information about different stages of the analysis.</li>
</ul>
<h2>6. Viewing Results</h2>
<h3>Using Mango for Visualization:</h3>
<ul>
<li>Download and install Mango from <a href="http://rii.uthscsa.edu/mango">Mango</a>.</li>
<li>Open the anatomical template file (Talairach or MNI) in Mango.</li>
<li>Add the thresholded results image as an overlay.</li>
<li>Update the image range to ensure all results are shown.</li>
<li>Enable anatomical labels and coordinates display for better interpretation.</li>
<li>Adjust the color map for better visualization of the results.</li>
</ul>
<h2>7. Additional Analysis Options</h2>
<h3>Connectivity Analyses:</h3>
<p>Use meta-analytic connectivity modeling (MACM) to examine the functional connectivity of a specific brain region.</p>
<p>For more information: <a href="https://www.brainmap.org/pubs/RobinsonHBM10.pdf">Robinson HBM 2010</a></p>
<p>For detailed instructions, refer to the full GingerALE user manual available in the BrainMap website: <a href="https://www.brainmap.org/ale/manual.pdf">GingerALE Manual</a></p>
<p>VIDEO TUTORIAL: <a href="https://www.youtube.com/watch?v=Zt0qrrI4EVI">GingerALE Tutorial</a></p>
<img src="images/Meta-analysis_process.png" alt="Worflow" style="width: 65%;">
<p>Image. <em>Workflow stages of the activation likelihood estimation (ALE) method</em></p>
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<h2>Funding</h2>
<p> We would like to express our heartfelt gratitude to <strong>Neurohackademy</strong> at the <strong>University of Washington eScience Institute</strong> for providing invaluable training and support. This experience has significantly enriched our understanding of neuroimaging and data science. We also acknowledge the support of the National Institute of Mental Health (NIMH) grant number <strong>5R25MH112480-08</strong>, which made this opportunity possible.</p>
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