In the past, I’ve posted on creating ROIs in AFNI and ways to manipulate those ROIs once created. But something that comes up fairly often on the AFNI message boards is how to use 3dcalc to create different ROI shapes. The most common that I’ve found are creating spheres and cubes, I’ve made some crazy […]
Creating ROIs in AFNI with Coordinates
Posted by pete on February 5, 2014
https://blog.cogneurostats.com/2014/02/05/advanced-creation-of-rois-in-afni/
TORTOISE Processing of DWI/DTI (Part 2)
Last time, we covered how to use TORTOISE’s DIFF_PREP tool to preprocess Diffusion Weighted Images (DWI) to correct for eddy currents, motion, rotate the b-vectors (alongside the motion correction), and optionally correct b-splines if we used a T2-weighted structural image. The next step is to use DIFF_CALC to fit tensors, inspect the results, measure ROIs, […]
Posted by pete on January 23, 2014
https://blog.cogneurostats.com/2014/01/23/tortoise-processing-of-dwidti-part-2/
TORTOISE Processing of DWI/DTI (Part 1)
These instructions are for an older version of TORTOISE, if you would like to read new instructions checkout the updated tutorial HERE! There are many options when deciding how to process Diffusion Weighted Images (DWI) and turn them into Diffusion Tensor Images (DTI). I’ve written before about preprocessing in FSL (Part 1, Part 2) and AFNI (Part […]
Posted by pete on January 3, 2014
https://blog.cogneurostats.com/2014/01/03/tortoise-processing-of-dwidti-part-1/
Year 1 Reflection
I really started investing in this blog in November 2012. In the first month it received 12 hits. In the second month, it also received 12 hits. But as we’ve added more content over the past year, the number of hits has continued to go up. And I’m very happy that today, we celebrate more […]
Posted by pete on December 3, 2013
https://blog.cogneurostats.com/2013/12/03/year-1-reflection/
Statistics on the Brain with AFNI
In previous posts I’ve covered how to use AFNI to run GLMs on your data to find task-related activations. But there are a host of other statistics that you can run on the brain outside of the GLM! And this is where AFNI really shines in terms of having a diverse set of tools, yet […]
Posted by pete on November 25, 2013
https://blog.cogneurostats.com/2013/11/25/statistics-on-the-brain-with-afni/