Waisman Brain Imaging Lab Tutorials:

• AIR (coregistration)
• AFNI:
  • Introduction emphasizing the GUI. (PDF format, by Hillary Schaefer)
  • Single subject block-design tutorial (by Tom Johnstone).
• BESA
• BrainVoyager
• Coregistration:
  • Coregistration lecture (in PDF format).
  • Coregistration of EPI, T1 data to MNI template.
  • AIR tutorial
  • BrainSqueezer manual coregistration
• Demo pictures for lab tours.

• Finding the Anterior Commissure (AC) and Posterior Commissure (PC), by Wil Irwin.

• Functional MRI Analysis Guidelines
  • Coregistration Manual (EPI, T1 data to MNI template).
  • Directory Structure guidelines for how to store data.
  • FIP User's Manual, the GUI interface for launching fMRI reconstructions.
  • multistatic: voxelwise covariates to correct for grey-matter probability contribution to functional "activations".
• IDL
  • Spamalize/IDL primer.
  • IDL's Object programming.
• PET
  • Introduction to PET acquisition (an alternative to getting it from an animal shelter).
  • FDG Quantitation Tool and primer.
  • Functional Imaging with PET.
• Python Software.
  • Python introduction.
  • Python tutorial for creating a brain image analysis batch script.
  • Terry Oakes' python libraries
  • Tkinter intro by Frederik Lundh
• Spamalize
  • BrainMaker: Intro to ROI drawing, help, and a tutorial.
  • BrainSpinner (3D spinning brains).
  • BrainSqueezer (coregistration).
  • Spamalize/IDL primer.
• SPM
  • fMRI analysis (Adobe .pdf).
  • fMRI visual stimulation analysis for a single subject block-design.
  • Slice Timing Correction (for coronal acquisition).
• Unix/linux

• Introduction to unix/linux
• scripting programs
• window manager settings

External Tutorials:

• fMRI
  • fMRI for Dummies, by Jody Culham, Ph.D., University of Western Ontario.
  • fMRI course by Luis Hernandez, Tom Nichols, & Doug Noll at University of Michigan
  • fMRI analysis tutorial, by Rajeev Raizada at Harvard Medical School
  • MRI and fMRI primer, by Doug Noll at University of Michigan
• Python:
  • Tkinter intro by Frederik Lundh

Software links, Downloads:

These may not link you directly to the software you are looking for, but will point you in the right direction.

• Spamalize

• fMRI Tools: Scripts for fMRI batch data analysis
• Voxelwise covariates: Correcting functional results for presence/absence of GM tissue. Contact Terry Oakes for download details.
  
• Rhesus monkey brain atlas from:
  • McLaren, DG, Kostmatka, KJ, Oakes, TR, Kroenke, CD, Kohama, SG, Matochik, JA, Ingram, DK, and Johnson, SC. A Population-Average MRI-Based Atlas Collection of the Rhesus Macaque. Neuroimage (in press-2008).

Please send suggestions to troakes - at - wisc.edu

Back to Software page.