Quite a few tools for processing MRI data take considerable amounts of time to run, even with computer hardware getting faster and cheaper daily. I have previously discussed how to queue up multiple Freesurfer jobs with GNU Parallel in order to automatically queue and dispatch a number of Freesurfer processes simultaneously. But what do you […]
All posts in category Programming
Tips for Remote Processing
Posted by pete on July 29, 2013
https://blog.cogneurostats.com/2013/07/29/tips-for-remote-processing-of-mri-data/
Parallelizing Freesurfer
Today I started running VBM and Freesurfer comparisons on a “new” dataset that everyone in our lab is particularly interested in moving forward. The VBM was all carried out in SPM8 with the VBM8 toolbox. I particularly like the VBM8 toolbox because it makes use of the SPM8 DARTEL transformations, and it’s relatively easy to queue up […]
Posted by pete on June 10, 2013
https://blog.cogneurostats.com/2013/06/10/parallelizing-freesurfer/
Source Code Available
Some time ago, I made available a series of custom-built software packages for helping perform EEG/ERP Analysis. I have now finished uploading the source code to my github repository. All of the programs were written in Objective-C, many of them fairly early in my programming career (forgive the comments or lack of comments!). If you […]
Posted by pete on May 21, 2013
https://blog.cogneurostats.com/2013/05/21/source-code-available/
Using R with AFNI
AFNI already has a host of programs that use R to analyze MRI data – 3dLME, 3dMVM, 3dMEMA, etc. Suppose you wanted to create your own functions that use R to manipulate data – well here’s a quick introduction. In this quick example, here is how to “Auto Mask” your dataset in R. source(‘path/to/AFNI/AFNIio.R’) thedata […]
Posted by pete on April 9, 2013
https://blog.cogneurostats.com/2013/04/09/using-r-with-afni/
Using the GNU Scientific Library with Xcode
The GNU Scientific Library (GSL) includes convenient use to matrices among other things. One convenient way to install GSL is using homebrew. Once installed a quick “brew install gsl” will do the work for you. To then use GSL with Xcode, do the following: Create a new Xcode Project Edit Build Settings Under “Other Linker […]
Posted by pete on December 30, 2012
https://blog.cogneurostats.com/2012/12/30/using-the-gnu-scientific-library-with-xcode/