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
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
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
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