This book, Andy’s Brain Book, is the ReadTheDocs companion to Andy’s Brain Blog. It is intended for fMRI beginners, with more advanced imaging techniques being added later on. If this is your first time here, watch this video for a quick overview of the website.

Aug 4, 2014 · In any case, DTI data takes some time to clean up before you can do any statistics on it. However, the preprocessing steps are relatively few, and are analogous to what is done in a typical FMRI preprocessing pipeline. The steps are to identify and correct any distortions during the acquisition, and then to correct for eddy currents.

MRtrix is a software package for analyzing diffusion data. One of the notable advantages of MRtrix over tensor-fitting techniques is their method of constrained spherical deconvolution, or CSD; this method deconvolves the diffusion signal in each voxel into a …

Preprocessing removes sources of noise from the image, such as movement artifacts and other distortions.

A common use of DTI is to compare different populations, such as young and old, and to observe where fractional anisotropy (FA) differs between groups, possibly with the assumption that less FA can be indicative of less efficient communication between cortical regions.

Aug 4, 2014 · In any case, DTI data takes some time to clean up before you can do any statistics on it. However, the preprocessing steps are relatively few, and are analogous to what is done in a typical FMRI preprocessing pipeline. The steps are to identify and correct any distortions during the acquisition, and then to correct for eddy currents.

Jul 8, 2012 · Given a resting state fMRI dataset and a parcellated brain volume image in DTI space, please design an algorithm to measure the functional connectivity between those parcellated brain regions. 1) The data is already transformed to the same DTI space. 2) The brain volume is parcellated into anatomical regions based on the HAMMER algorithm.

Aug 6, 2014 · Instead of going through each DTI analysis step individually, I've collated everything into a Youtube playlist down below.

Aug 6, 2014 · Instead of going through each DTI analysis step individually, I've collated everything into a Youtube playlist down below.

To run the command eddy, we will need to create two more files, in addition to what we have already generated. The first is a mask of the image that we will use with eddy, which should be based on the corrected dataset that we generated using topup in the previous section. We will begin by extracting the first volume of that dataset using fslroi: