diff --git a/docs/guide/Project/Specification.md b/docs/guide/Project/Specification.md index 263979d..15207cc 100644 --- a/docs/guide/Project/Specification.md +++ b/docs/guide/Project/Specification.md @@ -3,6 +3,62 @@ title: Specification sidebar_position: 2 --- -## Work in progress! +# Meta-Analysis Specification -We're still working on completing the documentation for this. Please check back later. +Now that your studyset's studies have all the necessary information (metadata, coordinates, annotations), you can configure and run a meta-analysis! + +A wizard will guide you through the following key steps of meta-analysis specification. + + + + +### 1) **Select the Algorithm and Corrector** + *Choose the algorithm for your meta-analysis and, optionally, select a statistical correction method (corrector).* + + Neurosynth-Compose supports several meta-analysis algorithms, powered by NiMARE, a Python library for neuroimaging meta-analysis. + For an overview to the coordinate-based meta-analysis methods supported by NiMARE, [refer to this guide](https://nimare.readthedocs.io/en/stable/cbma.html). + + Supported coordinate-based methods include: + + - **MKDADensity** (default): Multi-Kernel Density Analysis. A popular density-based meta-analysis algorithm. Creates a binary sphere around each coordinate. + - **ALE**: Activation Likelihood Estimation, convolves coordinates with a 3D Gaussian distribution. + - **MKDAChi2**: Allows you to compare your meta-analysis studies with a larger reference set of studies. It tests whether a higher proportion of studies in your meta-analysis activate a specific voxel compared to a larger population of studies that were not included. For more details, [**see the MKDAChi2 Association tutorial**](/compose-docs/tutorial/advanced/mkda_association) + + For each algorithm, a default set of arguments is used, but you can easily modify them. For a complete reference on available arguments, see the [NiMARE API Docs](https://nimare.readthedocs.io/en/latest/api.html#nimare-meta-meta-analytic-algorithms). + +Next, select a method for [multiple comparisons correction](https://nimare.readthedocs.io/en/latest/cbma.html#multiple-comparisons-correction): + + + - **FDRCorrector** (default): False Discovery Rate correction. + - **FWECorrector**: Family-Wise Error Rate correction. We strongly recommend using FWECorrector for publication-quality results with 10,000 iteration if possible. This is computationl intesive, however, hence not the default option. + +![Wizard 1](/guide/specification_wizard1.png) + + +### 2) **Select Analyses** + Now you will select which studies & analyses you want to include in your meta-analysis. To do so, select the annotation column for inclusion, which determines which analyses are used in the meta-analysis. B + y default, the "included" column contains all studies and analyses, but you can modify this based on your needs by editing `Annotations` in the Extraction step. + + A preview of the included studies based on the selected annotation column will be displayed. + +![Wizard 2](/guide/specification_wizard2.png) + + +### 3) **Meta-Analysis Details** + Enter a name and description for your meta-analysis to help you find it later. A default name will be provided, but you can customize it as needed. + +### 4) **Review** + Finally, you can review your selected options before creating your specification. + +![Wizard 3 Review](/guide/specification_wizard3.png) + +### 5) **Finalize** + To complete the specification process, click the "Create Meta-Analysis Specification" button. + +--- + +## Running the Meta-Analysis + +After clicking "Create Meta-Analysis Specification," you will be taken to a page displaying the status of your running analyses. Refer to the next section of the documentation for details on running and monitoring your meta-analysis. + +--- diff --git a/static/guide/specification_wizard1.png b/static/guide/specification_wizard1.png new file mode 100644 index 0000000..58a3da1 Binary files /dev/null and b/static/guide/specification_wizard1.png differ diff --git a/static/guide/specification_wizard2.png b/static/guide/specification_wizard2.png new file mode 100644 index 0000000..1ee96bd Binary files /dev/null and b/static/guide/specification_wizard2.png differ diff --git a/static/guide/specification_wizard3.png b/static/guide/specification_wizard3.png new file mode 100644 index 0000000..99d1265 Binary files /dev/null and b/static/guide/specification_wizard3.png differ