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Update Appendix_B_BiasedAnalysis.rst
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andrewjahn committed Aug 13, 2023
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Expand Up @@ -76,10 +76,12 @@ The two most popular ways of creating unbiased ROIs are:

AFNI and FSL each come with their own set of atlases (for SPM, you will need to download a separate toolbox first). To learn more about how to use each of these package's atlases, follow these links to the tutorials on :ref:`AFNI <AFNI_09_ROIAnalysis>`, :ref:`FSL <fMRI_09_ROIAnalysis>`, and :ref:`SPM <SPM_09_ROIAnalysis>`.

A spherical ROI is creating by noting the coordinates of the peak activation reported by another study. Ideally, this should be a study that uses an experimental identical to the one that you use, or at least is very similar. In most cases, you will have to find a study that uses an experiment that at least taps into the same cognitive process that you are studying. Methods for creating spherical ROIs can also be found in the same links just referenced.
Spherical ROIs are created by noting the coordinates of the peak activation reported by another study. Ideally, this should be a study that uses an experimental identical to the one that you use, or at least is very similar. In most cases, you will have to find a study that uses an experiment that at least taps into the same cognitive process that you are studying. Methods for creating spherical ROIs can also be found in the same links just referenced.

A third way of creating unbiased ROIs is to use a meta-analysis map, which represents a combination of individual statistical maps reported by hundreds or thousands of studies. The most accessible meta-analysis generator is `Neurosynth <neurosynth.org>`__, which allows you to generate these maps in seconds. For more details on how to create these maps, see :ref:`this tutorial <Appendix_E_Meta_Analysis>`.

Lastly, you can create an ROI from a contrast generated in a specific run of the experiment, usually called a **localizer** scan (not to be confused with an anatomical localizer, which is often used to help acquire the final anatomical scan).


Other Types of Biased Analysis
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