Day 1 Practicum: BrainMap Materials

Taxonomy

The BrainMap Taxonomy describes the experimental design of neuroimaging publications. It has many parts, but in particular:

Scribe

Scribe prepares publications for entry into our databases by encoding them using our taxonomy.

The latest version of the software is available from brainmap.org/scribe.

Scribe manual: manual_sparse.pdf

Scribe Training Videos (zip files):

Scribe example files:

Sleuth

Sleuth searches our databases, creates "workspace" data-sets, plots coordinates in Talairach space, and supports exporting data for further analysis.

The official version can be downloaded from brainmap.org/sleuth.

There is also a pre-release version of Sleuth. It includes a "filter" search field that lets you quickly find studies within your workspace and refine your dataset.

Sleuth manual: manual.pdf

Sleuth requires a user account, but for the workshop you can use:
User: workshop
Password: workshop16

Sleuth Training Video (zip files):

GingerALE

GingerALE can perform analyses in Talairach or MNI space, and includes a tool for converting between them. Several thresholding options are available: P value, Family-wise Error (FWE) correction by voxel-wise ALE value or by cluster-size. Areas passing the threshold are described in "cluster stats". It is also useful for meta-analytic connectivity analysis (MACM).

The latest version can be downloaded from brainmap.org/ale

GingerALE manual: manual.pdf

GingerALE example files:

PRISMA Consort Spreadsheet: PRISMA_TABLE_MDD_example.xlsx

Day 2 Practicum: Mango Materials

Mango

Mango is a powerful image viewing and analysis program.

The latest desktop version is available for download.

Behavioral Analysis and Paradigm Analysis can be added to Mango as plug-ins.

Mango example files:

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