AZTEC – Cardiorespiratory correction software for functional MRI

T.E. Gladwin, M. van Buuren & M. Vink

Aztec removes confounds due to cardiac pulsation and the respiratory cycle using RETROICOR. In addition, it removes confounds due to fluctuations in heart rate, heart rate variation and respiration volume per unit time (RVT) using a multiple regression approach.

Aztec is programmed in Matlab and requires SPM (either SPM2 or SPM5) to be in the path. The built-in parseLog function is used to calculate the cardiorespiratory variables from the measured ECG and respiration signal.

Download

DESIGN MAGIC – evaluate your design matrix and calculate the optimal high-pass filter

M. Vink

Design Magic (d_magic) calculates the multicolinearity indices for all factors of a design matrix generated in SPM (version 2/5/8). In addition, it calculates the optimal cut-off for the high-pass filter commonly used in fMRI research to remove low drifts in the signal.

The idea behind the program is that is allows users to evaluate their design in terms of uniqueness of the factors. In this way, one can make an optimal design prior to scanning, in terms of minimising overlap between factors. Another issue important for obtaining an optimal design is the amount of variance for each factor. This is not calculated, but will be incorporated in the next version of the program.

After selecting an SPM.mat file, the program will calculate the R^2 value for each factor. This value indicates how much variance is shared with the other factors in the design. An R^2 value of .33 means that 33 percent of the variance of that factor is also explained by (any linear combination of) the other factors. Generally, it is a good thing to keep the R^2 for each factor low so that each factor explains as much unique variance as possible.

These R^2 values are also used to evaluate the impact of the high-pass filter, which is made up of cosine function. The program will let you test your own high-pass filter as well as calculate the optimal cut-off for the filter.

Download

READER – Preprocessing & Statistical Analysis of functional MRI data

M. Vink

When I started doing functional MRI research, I found it very difficult to get a concise overview of all the information relevant for doing preprocessing and statistical analysis. Therefore, I started writing this reader, collecting information and learning along the way. The basics that are described are still valid, although the reader as a whole is a little bit outdated. For example, slice-timing is not included (yet).

Download