Contents
Step by Step Guide
Resting state analysis (with dual regression)
Initial processing (dicom conversion, fslreorient2std, brain extraction for structurals)
[ Optional: denoise individual datasets with FIX or via manual classification and denoising ]
Run concat ICA via the Melodic GUI for all sessions/subjects (go through each tab and fill in appropriate information)
Misc tab: defaults are fine
Data tab: select session/subject dataset (if multiple sessions per subject exist then include individual sessions as separate inputs, and do not concatenate the data)
Pre-Stats tab: the defaults here represent our general recommendations
Registration tab: we recommend using a Main structural image, with BBR, plus nonlinear registration to the Standard space
Stats tab: select Multi-session temporal concatenation
Post-Stats tab: the settings here are unimportant in this instance
- Check the webpage output, especially the registrations
- Look at output components and decide what networks are of interest
- Run the Glm GUI (for higher-level analysis)
Setup an appropriate group design (e.g. unpaired group difference) - the Wizard offers some simple/common designs
Save the design (need .mat and .con files later)
Run the dual_regression script, from the directory where the melodic outputs were written (use the GLM design files, melodic_IC image, .filelist file)
- Look at the outputs from dual regression
These outputs are from randomise and the *corrp* images are the crucial ones to view (these are the multiple comparison corrected p-values, stored as 1-p values)