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
Note: There are faster (and better) methods than this for creating volumetric masks from aseg labels. I wrote this guide in part to demonstrate some of the features of multiple imaging programs. See this post for a faster method. You … Continue reading
Suppose you ran recon-all (the main command in FreeSurfer for automated processing) on a number of participants’ MRIs and now wanted to convert one or more of the cortical parcellation areas to a volumetric mask for manual cleaning of the structure or … Continue reading
Understanding the bash environment and simple bash scripting can really speed up your neuroimaging work. While I am not an expert in scripting, I have learned a few tricks that can make life easier. If you are interested in learning … Continue reading
Note: While I will try to be verbose in my how-to guides of imaging, I assume any readers have at least basic knowledge of the command line (Terminal) and bash. If you feel lost with some of the bash references … Continue reading