If you’re reading this post either you’re a loyal fan (yay!) or you’ve run Freesurfer (possibly in parallel) and processed your diffusion data in (hopefully TORTOISE) and then Tracula (also possibly in parallel) and you’re wondering where do you go from here. I’m glad you’re here, that’s probably me talking to myself because I read my own blog […]
All posts in category DTI
DTI Statistics with TRACULA data (Part 1)
Posted by pete on May 22, 2017
https://blog.cogneurostats.com/2017/05/22/statistics-with-tracula-data-part-1/
Preprocessing Diffusion Weighted Images with TORTOISE 3 (Part 1)
A while back, I posted about how to use TORTOISE 2.0/2.5 for preprocessing Diffusion Weighted Images (DWIs), create tensors, and then do blip-up blip-down correction. All of those steps relied on using a graphical user interface (GUI) through a program called IDL to tell TORTOISE what you wanted it to do. This was often a […]
Posted by pete on April 10, 2017
https://blog.cogneurostats.com/2017/04/10/preprocessing-diffusion-weighted-images-with-tortoise-3-part-1/
Parallelizing Tracula
By popular request, or rather the sheer number of hits the Parallelizing Freesurfer post, today we turn our attention to Tracula, the Freesurfer integrated solution for doing diffusion tensor imaging (DTI) tractography! Tracula has a lot of nice features, one of my favorites is the ability to estimate 18 or so tracts in the brain by constraining […]
Posted by pete on August 11, 2015
https://blog.cogneurostats.com/2015/08/11/parallelizing-tracula/
How to Analyze Diffusion Tensor Imaging Data (Review)
After my first year of blogging, I ran a “One Year Review” piece that covered all of the articles that I wrote in that first year. And that article tends to get hit by search engines fairly often since it was published on December 3, 2013. Sure, I meant to go back and do a […]
Posted by pete on June 29, 2015
https://blog.cogneurostats.com/2015/06/29/how-to-analyze-diffusion-tensor-imaging-data-review/
Example use of DTIprep for DWI Quality Checking
In a previous post, we covered using DTIprep for preprocessing of diffusion weighted imaging (DWI) data. I’ve written a quick script (below) to automate DTIprep for the purposes of running the default QC check. My workflow has DICOM data automatically downloaded from our PACS server, then automatically converted to NIFTI format, and then organized in the […]
Posted by pete on April 16, 2015
https://blog.cogneurostats.com/2015/04/16/example-use-of-dtiprep-for-dwi-quality-checking/