I know I post a lot about registration (see here and here) but I believe that image registration is one of the most important components of an MRI processing pipeline. Thankfully, there are some good tools available. FLIRT, FNIRT, bbregister, … 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
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
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