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This wiki's purpose is to provide documentation about the use of software at the CIC, and to provide reference for Cobra Laboratory.

MAGeTbrain	CIVET
Running MAGeTbrain and MAGeTbrain Morpho	Cortical Thickness & Surface Analysis with CIVET
Best Templates for MAGeT	VBM with CIVET
Demographically Stratified Templates for MAGeT	Sampling Multimodal Data onto CIVET Surfaces
MAGeTbrain Guide to QC Rating
MAGeTbrain Morphology Analysis	Extracting Global Gray Matter, White Matter and CSF volumes from CIVET
Generating MAGeTbrain QC Images	ROI Analysis in CIVET

Rodent Imaging	Misc
DICOM to MINC Conversion	Finding an optimal mixed effects model
Mouse Scan Preprocessing
Two level model building (Old)
Two level model building on Niagara (Old)
Rodent fMRI ‐ gICA & DR: Processing & Visualization
Rodent fMRI ‐ Generating Seeds for Seed Based Connectivity
Rodent fMRI‐ Functional Connectivity Between Networks or Regions