From The CNBC Wiki
Jump to: navigation, search

Random links that you might find useful...


The best software solution for running psychophysical experiments (requires Matlab)

  • PsychToolbox's home site
  • Open source site for PsychToolbox
  • ExpToolbox (.zip archive) is a random collection of routines written by Michael Tarr to work with PsychToolbox. The key routine is readdata which makes reading in text files somewhat less painful. Now includes an improved readdata routine (v 1.3).
  • If you don't like or can't use PsychToolbox, check out this useful page summarizing many different packages/tools for use in visual psychophysics.

Stimulus Manipulation

Free and almost free software for manipulating images or sounds

Code and manual for: Willenbockel, V., Sadr, J., Fiset, D., Horne, G. O., Gosselin, F., & Tanaka, J. W. (2010). Controlling low-level image properties: The SHINE toolbox. Behavior Research Methods, 42(3), 671-684.
  • Audacity® is free, open source software for recording and editing sounds. It is available for Mac OS X, Microsoft Windows, GNU/Linux, and other operating systems.
  • GraphicConverter converts images between *many* different formats. It also offers many useful features for image manipulation and viewing.
  • GIMP is the GNU Image Manipulation Program. It is a freely distributed piece of software for such tasks as photo retouching, image composition and image authoring. It works on many operating systems, in many languages. Think of it as a poor-man's photoshop.
  • Xee is a lightweight, fast and convenient image viewer and browser.
  • RCM Tools implements image processing with natural scene statistics. From the Center for Perceptual Systems at the University of Texas.
  • Phatch equals photo batch! A nice open-source photo batch processor. Offers most functions you would ever need.


Useful pages and code to learn about and to run neuroimaging studies

  • fMRI 4 Newbies is a very clear and understandable "crash course in brain imaging".
  • practiCal fMRI is a site with lots of information, tips and tricks to help you conduct better fMRI experiments.
  • I Do Imaging is a database of free medical imaging software.
  • Simitar is a toolbox developed at the Botvinick Lab by Francisco Pereira, designed to examine neural similarity patterns using a "searchlight" around each voxel.
  • Surfing is a Matlab toolbox for surface-based voxel selection, providing functionality for surface-based multivariate information mapping of the cerebral cortex using fMRI data.

Computational Stuff

Resources to aid in learning about various computational approaches


Statistics packages and learning tools

  • |Stat ("pipestat" or unixstat) is one of the easiest to use stat packages around and it is the free. It is entirely command-line based, deceptively simple, and the best tool out there for fast data manipulation. Gary Perlman (|STAT's author) distributes both DOS and UNIX versions for free, below is a somewhat dated recompile for OS X.
    • |Stat's home site and Web-based man pages
    • OS X binaries (zipped tar archive). I have recompiled the source for Mac OS X if anyone is interested. I never heard back from Gary about distributing the OS X versions, so I have made the binaries and the associated man pages available. Included in this distribution are several variations on the original version. Specifically, I have created four "new" commands: dl, ttest, mpttest, and a new, improved anova (that reports true n's and can automatically compute cell means by subjects). The man page for anova reflects this change. dl is self-documenting via "dl -h" and ttest and mpttest are simply that - they take two columns of numbers and return the appropriate statistic. I recommend putting these binaries in /usr/local/bin (which should already be in your PATH, but if not add it). NOTE: These have recently been recompiled for 64 bit Intel Macs - they seem to work fine, but they have not been extensively tested.
    • man pages (zipped tar archive). I recommend putting these man pages in /usr/local/share/man/man1 (which you definitely will need to add to your MANPATH).
  • The R Project. R is a language and environment for statistical computing and graphics. It is a GNU project which is similar to the S language and environment which was developed at Bell Laboratories (formerly AT&T, now Lucent Technologies) by John Chambers and colleagues. R can be considered as a different implementation of S. There are some important differences, but much code written for S runs unaltered under R. RStudio makes it even better!
  • OpenLearningInitiative from Carnegie Mellon offers Open & Free Courses for independent learners and includes self-guiding materials and activities that are freely available. Plus, they are available all the time so you can learn at your own pace. Courses include:
    • Introductory Statistics
    • Statistical Reasoning
  • WISE. Web Interface for Statistics Education - Courtesy of Claremont Colleges.
  • Gephi. An interactive visualization and exploration platform for all kinds of networks and complex systems, dynamic and hierarchical graphs.

Useful Random Stuff

Free (or almost free) and useful software tools

  • TextWrangler is a General Purpose Text Editor | Programmer's Text Editor | Powerful Text Transformer and Manipulator | Courtesy of BareBones Software.
  • Name Mangler is a batch file renamer. It supports the following basic renaming routines: Find and replace (including support for regular expressions); Number sequentially; Change case; Set extension; Add prefix/suffix; Remove/insert characters; plus a wide variety of other useful functions. It now costs $10 through the Mac App Store - worth every penny.
  • LineBreak is a simple utility for Mac OS X that converts line breaks in text documents. It can convert to Mac, UNIX®, and Windows/DOS formats. It is written entirely in Cocoa and supports drag and drop from the Finder. LineBreak is a Universal Binary (works on PPC and Intel Macs).