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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