There are plenty of points in ERP data analysis that can be subjective. But that doesn’t mean that they have to be! One subjective point is determining the noise level of your subjects. If you’re using Net Station (EGI), you can check an option in the “Averaging” Waveform tool to calculate noise estimates. This will […]
All posts in category Neuroimaging
Finding ERP Noise Outliers
Posted by pete on September 9, 2013
https://blog.cogneurostats.com/2013/09/09/finding-erp-noise-outliers/
Rotating bvecs for DTI fitting
Update: While these methods continue to be useful, I now recommend using TORTOISE for preprocessing DTI. The TORTOISE pipeline includes methods for (among other things) reducing distortions from EPI artifacts, eddy current correction, correcting for motion, rotating b-vecs, and co-registration to an anatomical image. There are instructions for using the newest version here. Most […]
Posted by pete on September 6, 2013
https://blog.cogneurostats.com/2013/09/06/rotating-bvecs-for-dti-fitting/
Creating AFNI images via command line and Xvfb
Quite a while ago, I wrote a post about making automated snapshots of MRI activation with AFNI. One of the things I always appreciated about FSL was that they provided a series of ready-made images to show off where activation was in the brain for a given analysis (at least using FEAT). So when I […]
Posted by pete on September 3, 2013
https://blog.cogneurostats.com/2013/09/03/generating-activation-maps-in-afni-without-opening-x11/
Analyzing DTI Data in AFNI (Part 2)
While the information in this post is useful, I recommend users use TORTOISE for processing diffusion data. You can read a tutorial of TORTOISE3 here. I previously described how to do some DTI analyses in AFNI. To review, we could use a linear alignment to the b0 image in order to correct for some eddy […]
Posted by pete on August 26, 2013
https://blog.cogneurostats.com/2013/08/26/analyzing-dti-data-in-afni-part-2/
Writing your own fMRI programs using the AFNI API (Part 1)
I find that it’s fairly rare that I wish there was an AFNI program that did something that cannot be accomplished with existing tools and a bit of creativity. But, if you do find something that requires writing a custom program, the AFNI distribution is both easily accessible and fairly straightforward to code for. Over […]
Posted by pete on August 21, 2013
https://blog.cogneurostats.com/2013/08/21/writing-your-own-fmri-programs-using-the-afni-api-part-1/