Day 1 Practicum: BrainMap Materials
The BrainMap Taxonomy describes the experimental design of neuroimaging publications. It has many parts, but in particular:
- Types of papers: eligibility, functional and structural, sparse coding
- Behavior Domains: the cognitive behavior isolated by the experiment
- Paradigm Classes: the type of task the subjects perform
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:
- Adank Neuropsychologia 2012: [pdf] [ent]
- Fang Human Brain Mapping 2009: [pdf] [ent]
- Han Journal of Affective Disorders 2014: [pdf] [vbm]
Sleuth searches our databases, creates "workspace" data-sets, plots coordinates in Talairach space, and supports exporting data for further analysis.
The latest version can be downloaded from brainmap.org/sleuth.
Sleuth manual: manual.pdf
Sleuth requires a user account, but for the workshop you can use:
Sleuth Training Video (zip files):
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 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:
- Analysis: [43MB zip]
- Interpretation: [48MB zip]
- Visualization: [46MB zip]
- GingerALE example results: [1.5MB zip]