Before anyone undertakes research where diffusion weighted MR imaging will be done, I think he or she should read a 2010 article by Derek K. Jones and Mara Cercignani. This article – Twenty-five pitfalls in the analysis of diffusion MRI data … Continue reading
Here are a few of my favorite fiber tracking images I’ve created (and one non-diffusion image). There is an art to neuroimaging. Sorry for the obnoxious watermarks; because all the images are funded by the grant NINDS K23NS060660 (Catherine Price, University … Continue reading
FreeSurfer includes a useful tool for manipulating mask files. Let’s say you wanted to pull the left caudate from the aseg.mgz file in order to use it for fiber tracking (that’s my default example in part because it’s salient for … Continue reading
I’ve written about Bash scripting previously, as it applies to neuroimaging. Scripting is extremely useful; it can save hours worth of work. But what if you want to do something that is repetitive but do not really need to create … Continue reading
I created this brief video of the cingulum. I am posting it here because it showcases some of the diffusion scan fiber tracking we do. The brain is that of a >60 year old male who is part of our … Continue reading
Image registration when working with multimodal neuroimaging or even different sequences within subjects is one of the most important parts of image processing. I’ve written about registering brain ROIs that were created in T1 space into diffusion space using FreeSurfer’s … Continue reading
You can now download version 5.0 of FreeSurfer! Link This looks like an exciting update to the program. I have not yet had an opportunity to play around with it other than to start a recon-all run on a subject. … Continue reading
One of my main interests in neuroimaging is diffusion MRI fiber tracking. There are multiple methods for tracking including ones based on a diffusion tensor (e.g., FSL’s FDT program). There are also other, more complex mathematical models for describing and … Continue reading
You can skip this first paragraph if you do not want to read a personal aside. One useful thing about becoming familiar with the command line interface (Terminal in OS X) is that a little scripting can save you days … Continue reading
In a previous post I wrote about converting FreeSurfer aseg (sub-cortical segmentation) labels to volumetric masks. I demonstrated a graphical way of pulling out individual labels; however, it can be fairly tedious. There are around 50 different labels in the … Continue reading