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 […]
All posts in category Neuroimaging
TORTOISE Processing of DWI/DTI (Part 1)
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/
The mysterious flipped brain
I previously reviewed a series of DICOM to NIFTI converters. The entire purpose of this post is to state how important it is to check the orientation of the images coming out of any DICOM to NIFTI converter. The example today illustrates an incorrect flip in dcm2nii, but I want to stress that this happens […]
Posted by pete on November 14, 2013
https://blog.cogneurostats.com/2013/11/14/the-mysterious-flipped-brain/
Quickly Creating Masks in AFNI
Often when creating a mask to use with 3dROIstats, 3dmaskave, or 3dmaskdump, we will create a mask at a higher resolution than our functional runs, detailed here. One of the reasons the mask is created at a higher resolution is that we base the anatomical masks on either 1) the high-resolution anatomical or 2) the […]
Posted by pete on November 5, 2013
https://blog.cogneurostats.com/2013/11/05/quickly-creating-masks-in-afni/