HowTos / Aps

Research specific applications available on the lab computers

Please see the system administrator for any questions about application availability and licensing.

Following is a list of software that we have installed on the linux machines (and some on the macs) that is most relevant to our lab (with the exception of matlab, which has its own pages for general help and our tools and data).

Cerebral Cortex Visualization Software

  • Caret - Application for cortical surface visualization and analysis. Caret, along with help and tutorials, is found in /usr/local/caret/. You can also visit the Van Essen web site for more information. Caret is also available on the lab macs. Further instructions for Caret can be found here.
  • Surefit - used for automated segmentation and surface reconstruction, in same directory as Caret, also created by the Van Essen lab. There is also an instructional pdf (/usr/local/SUREfit/instructions/SureFitUsersGuide.pdf), that may be useful to look at. Surefit is only available on the linux machines. To use these two software programs, make sure they are on your path, by checking that the following paths are in your .bash_profile or .profile (don't get rid of paths already there, just add caret and SUREfit paths): 
 export PATH=$PATH:/usr/local/caret/bin:/usr/local/SUREfit/bin

Image Processing

ImageJ - software from the NIH, for image processing and analysis in java. Located in /usr/local/ImageJ/. To start type imagej & in a terminal. ImageJ is available on both the linux machines and the mac (/Applications, just double-click).

Mathematica

- software for symbolic mathematics, located in /usr/local/Wolfram/Mathematica/5.0. To start mathematica, type mathematica & in a terminal for the gui, or type math in a terminal for the terminal version. For documentation visit the Wolfram web site. Mathematica is currently available only on the linux machines