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ACID toolbox

The Artefact correction in diffusion MRI (ACID) toolbox is an academic software toolkit for pre-processing of diffusion MRI data, estimation of DTI indices and normalisation of DTI index maps, which fully integrates into the batch system of SPM8. These tools are made for users familiar with the underlying statistical, mathematical and image processing concepts. The ACID toolbox provides the option to write the estimated diffusion tensor in the format of the Freiburg DTI tools.


The ACID Toolbox contains the following options:

Pre-processing of DTI data:


Tensor fitting:


FA-VBS Normalisation toolbox








The ACID toolbox is free but copyright software, distributed under the terms of the GNU

General Public Licence as published by the Free Software Foundation (either version 2, as given in file LICENCE.txt, or at your option, any later version). Further details on "copyleft" can be found at




This toolbox comes with absolutely NO WARRANTY! It is especially not intended for any clinical or diagnostic use.

Getting started


The toolbox requires Matlab and SPM8 to be installed on your computer. After downloading the toolbox archive, extract the files into your SPM/toolbox directory.


The archive contains four C-file "spm_hist2_z_exp_polyval2.c", "DTtoFA_nachHBM2010.c", "DTtoFA_2d.c", and "DTI2EVEW.c", which possibly have to be compiled before using. In order to do this, launch Matlab in the directory SPM/toolbox/ACID_tools/cfiles. Start the compilation by entering the command


mex spm_hist2_z_exp_polyval2.c

mex DTtoFA_nachHBM2010.c

mex DTtoFA_2d.c

mex DTI2EVEW.c



Eddy Current and Motion Correction

Mohammadi S, Moller HE, Kugel H, Muller DK, Deppe M (2010) Correcting eddy current and motion effects by affine whole-brain registrations: evaluation of three-dimensional distortions and comparison with slicewise correction. Magn Reson Med 64: 1047-1056; doi: 10.1002/mrm.22501.


Fit Diffusion Tensor

Mohammadi S, Hutton C, Nagy Z, Josephs O, Weiskopf N (2012), Retrospective correction of physiological noise in DTI using an extended tensor model and peripheral measurements. Magnetic Resonance in Medicine, (in press); doi: 10.1002/mrm.24467.


COVIPER combination of Diffusion Tensor

 Mohammadi S, Nagy Z, Hutton C, Josephs O, Weiskopf N. Correction of vibration artifacts in DTI using phase–encoding reversal (COVIPER). Magn Res Med 2012; 68: 882–889; doi: 10.1002/mrm.23308.


LPF correction of Diffusion Tensor

Mohammadi S, Nagy Z, Moller HE, Symms MR, Carmichael DW, Josephs O, Weiskopf N (2012), The effect of local perturbation fields on human DTI: Characterisation, measurement and correction. NeuroImage 60 (1): 562-570; doi: 10.1016/j.neuroimage.2011.12.009.


FA-VBS Normalisation toolbox

Ashburner J, Friston KJ (1999) Nonlinear spatial normalization using basis

functions. Hum Brain Mapp 7: 254-266.


Glauche V, Mohammadi S, Deppe M (2010) SPM normalization toolbox for

diffusion weighted images. Proc Intl Soc Mag Reson Med 18: Abstract


Mohammadi S, Keller SS, Glauche V, Kugel H, Jansen A, et al. (2012) The Influence of Spatial Registration on Detection of Cerebral Asymmetries Using Voxel-Based Statistics of Fractional Anisotropy Images and TBSS. PLoS ONE 7(6): e36851. doi:10.1371/journal.pone.0036851


Mohammadi S, Glauche V, Deppe M (2009b) SPM normalization toolbox

for voxel-based statistics on fractional anisotropy images. Proceedings of

the 15th Human Brain Mapping meeting, June 18-23, 2009, San

Fransisco, Neuroimage 47: S122.