AES-SDM reference manual

Introduction

This manual focuses on the software developed for the Seed-based d Mapping (formerly Signed Differential Mapping; SDM) method, an improved meta-analytic approach for voxel-based neuroimaging studies.

Index

	Introduction	Summary of the method and its main features.
	Preparation	Retrieved neuroimaging data must be included in a folder (see Preparing the folder), and information on samples, groups or variables must be introduced in the SDM table (see Creation of the SDM table). The last step of the preparation is the preprocessing of the studies and their Monte Carlo randomizations (see Preprocessing), preceded by a set of special steps in case of TBSS meta-analyses (see TBSS preprocessing).
	Globals analysis	You can conduct a (rather simple) meta-analysis of the global variables, e.g. the global gray matter in a meta-analysis of VBM studies, optionally adjusting for groups or covariates.
	Calculations	It is possible to calculate meta-analytic means (see Mean analyses), jackknife sensitivity analysis (see Jackknife sensitivity analysis), comparisons between groups including covariates (see Linear model analyses: comparing groups) and meta-regressions (see Linear model analyses: meta-regression).
	Results	Results from previous calculations can be thresholded obtaining meta-analytic peak coordinates, clusters breakdowns and NIfTI (Analyze-compatible) images (see Thresholding the results) which will be authomatically open in an MRIcron template (see Settings). Results of two meta-analyses of studies conducted in different modalities, e.g. VBM and fMRI, may be combined in a single map (see Multimodal meta-analyses). Results can also be extracted extracted from a Talairach label or coordinate (see Extracting masked values) using a mask (see Creation of a mask).
	Batch processing	You can easily save the commands you have used for later batch processing. Alternatively, you could create a script with your favourite language and call sdm.
	Settings	At the moment only one parameter must be specified to run SDM, the brain viewer, useful for authomatically seeing the results with MRIcron after thresholding.
	Running SDM as SPM extension	SDM can also be run as an SPM (Statistical Parametric Mapping) extension.
	How to cite	We have invested a lot of time and effort in creating SDM, please cite it when using it for a meta-analysis.