GitHub
I do not post here any more. Most of my MRI-related information is available on Github.
When not to mix results from FreeSurfer and FSL
Nyberg and colleagues (2015) report increased hippocampal volumes in PD (n = 21) versus non-PD peers (n = 20). Additionally, using FSL FIRST for a vertex analysis they found only right nucleus accumbens shape differences. The article is interesting in … Continue reading
Brain Template Creation with ANTs
These instructions use FA images to create an FA template using the software package ANTs (http://stnava.github.io/ANTs/); the process should work well with other image modalities. First we can use FLIRT to register a group of 4 brains (semi-randomly chosen by looking … Continue reading
Introduction to MRtrix 3
I’ve been trying out MRtrix 3 recently. It’s impressive software. I’ll post a guide about installing it and using it later but there is enough information to get started on the Google+ site, the GitHub repository (and associated sparse but growing wiki), and … Continue reading
FSL Version 5 in Mountain Lion
I just upgraded to FSL version 5 on my MacBook Pro running Mountain Lion. The installation was straightforward using the new install script from FMRIB: http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FslInstallation Download the python script and then in Terminal navigate to the download location and run: … Continue reading
Using awk to truncate text files
With neuroimaging analyses we deal with a lot of text files. These are often the result of program or scripts running on the MRI data; they can be statistics, volumes, error logs, or any number of other outputs. Let’s say … Continue reading
Using FreeSurfer’s bbregister for Image Registration
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
NeuroDebian
I recently came across a great resource for people involved in neuroscience research. It’s called NeuroDebian; it’s a Debian neuroscience repository. Debian is a popular Linux distro; what is likely the most popular consumer Linux distro – Ubuntu – is … Continue reading
A Great Resource for Advanced Bash Scripting
I’ve written about shell scripting before (see here and here). Scripting is necessary for efficient neuroimage processing. At the very least, it can provide a way to keep track of how you did something. While there are a number of … Continue reading
How much computer do you need for MRI processing?
I want to address how much computing power you need when imaging. The short answer is: as much as you can. RAM If you want to stick with a Mac environment, a Mac Pro would be ideal (although we use … Continue reading