This repository contains the implementation of all analyses in the manuscript Krohn S, Froeling M, Leemans A, Ostwald D, Villoslada P, *Finke C, *Esteban FJ. Evaluation of the 3D fractal dimension as a marker of structural brain complexity in multiple-acquisition MRI. Hum Brain Mapp. 2019;1–31. https://doi.org/10.1002/hbm.24599 Please refer first to the readme file which also illustrates the use of the demo function. The code has been tested for FSL version 5, Ubuntu 16.04, and Matlab version 2017b for Linux. Dependencies include the statistics and machine learning toolbox, parallel computing as well as the image processing toolbox, and NIfTI and ANALYZE tools (https://de.mathworks.com/matlabcentral/fileexchange/8797-tools-for-nifti-and-analyze-image). A function of the calcFD toolbox is used for box-counting (see Madan, https://github.com/cMadan/calcFD), and skeleton estimation is implemented with a 3D skeleton function (see Kollmannsberger, https://www.mathworks.com/matlabcentral/fileexchange/43400-skeleton3d). Other external subfunctions from FEX are appended and their use is made explicit where applicable. Please consider citing the above paper if you use any of the code.