Randomly, for those people who do a lot of manipulation of file names, it can be painful to constantly use sed or awk or basename to change the filename without the extension. Here are three options to copy a file via 3dcopy (part of AFNI, works just like cp, but for image files, will also […]
Dropping file extensions
Posted by pete on March 19, 2013
https://blog.cogneurostats.com/2013/03/19/dropping-file-extensions/
Converting DICOM files to NIFTI
Most people who are processing MRI/fMRI data will need to convert data from the scanner format DICOM to a more usable NIFTI format that is used by a variety of neuroimaging software packages (e.g. AFNI, FSL, SPM). As with most things in neuroimaging, there are a variety of options and here are a few (though […]
Posted by pete on March 18, 2013
https://blog.cogneurostats.com/2013/03/18/converting-dicom-files-to-nifti/
Correlating Brain and Behavior in AFNI
If previous posts hadn’t given it away, AFNI is my tool of choice for processing neuroimaging data. A lot of people get confused on the sheer number of options there are and that most things can be accomplished in a variety of ways. Today I’m going to outline three ways of doing Correlations between fMRI […]
Posted by pete on March 8, 2013
https://blog.cogneurostats.com/2013/03/08/correlating-brain-and-behavior-in-afni/
Agreement between software packages
Always nice when there is agreement between different neuroimaging packages. A quick block design analyzed in both AFNI and FSL – giving pretty similar results for the same participant. Both packages have distinct advantages. For AFNI: 1) it’s faster ; 2) it has more customizable options; 3) the viewer allows you to adjust […]
Posted by pete on January 3, 2013
https://blog.cogneurostats.com/2013/01/03/agreement-between-software-packages/
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/