USC Neuroscience Graduate Program
USC Neuroimaging Workshop
6/16/2011, Lei Liew (sliew@usc.edu)
Useful Links:
Searchable database of all tools available:
• NITRC:
• Internet Analysis Tools Registry:
• UCLA LONI Software:
Meta-Analysis:
• NeuroSynth:
• Ginger ALE:
• :
• AMAT (A meta-analysis toolbox):
• SumsDB:
• NIDAG:
fMRI-related Programs:
• BrainVoyager (need license):
• SPM (need matlab):
o Marsbar (ROI-based analyses):
o XJView (viewer + atlas):
o SimpleROIBuilder:
• FSL (need terminal access):
o PEATE (time-course):
o Most functions run from command line
• OptimizeDesign (Tor Wager’s genetic algorithm for planning designs): (it is called “Genetic Algorithm”)
• OptSeq (optimizing the jittered ITIs):
• Scripts for reading logfiles (ask me – we’ll put on a database soon)
• Batch scripts for most programs (ask me – we’ll put on a database)
Structural-related Programs and Viewers:
• MRICron (viewer, draws ROIs):
• MANGO (viewer, draws ROIS++):
• BrainSuite (detailed anatomical analyses, works with other programs):
• BrainVox (lesion analyses; hand trace):
• FSL (see above)
• FreeSurfer (cortical thickness; use with FSL):
• DTI – Dimitrios’s in house connection hub software (ask me!)
• Diffusion Toolkit/TrackVis:
• MedINIRA:
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