Matheon - F10: Image and signal processing in the biomedical sciences: diffusion weighted imaging - modeling and beyond

Package "fmri" for R

The R-package "fmri" provides functions for analyzing single run fmri data with structure adaptive smoothing procedure. This includes I/O function for ANALYZE, AFNI, or DICOM files, linear modelling with hemodynamic response functions, signal detection using Random Field Theory.

References: K. Tabelow, J. Polzehl, H.U. Voss, and V. Spokoiny. Analyzing fMRI experiments with structural adaptive smoothing procedures., NeuroImage 33(1), 55-62 (2006).
J. Polzehl, K. Tabelow. Structural adaptive segmentation of statistical parametric mapping NeuroImage 52(2), 515-523 (2010).
K. Tabelow, J. Polzehl, Statistical parametric maps for functional MRI experiments in R: The package fmri, J. Statist. Software, 44 1-21 (2011).

Documentation: J. Polzehl, K. Tabelow. Analyzing fMRI experiments with the fmri package in R. Version 1.0 - A users guide. WIAS-Technical Report No. 10 (2006), or J. Polzehl, K. Tabelow. fmri: A package for analyzing fmri data, RNews 7(2) 13-17 (2007).

Download: CRAN, which may contain a newer version, or fmri_1.4-0.tar.gz, or fmri_1.4-0.zip

Package "adimpro" for R

This packages provides functions for structure adaptive smoothing of digital images. This includes I/O functions for several image formats (including RAW), which relies on ImageMagick, image analysis and processing tools.

Reference, including documentation: J. Polzehl, K. Tabelow. Adaptive smoothing of digital images: The R package adimpro., Journal of Statistical Software 19(1), (2007).

Download: CRAN, which may contain a newer version, or adimpro_0.7.3.tar.gz, or adimpro_0.7.3.zip

Package "dti" for R

This package provides a structure adaptive smoothing procedure for Diffusion Tensor Imaging (DTI).

Reference: K. Tabelow, J. Polzehl, V. Spokoiny, and H.U. Voss. Diffusion Tensor Imaging: Structural adaptive smoothing, NeuroImage 39(4), 1763-1773 (2008).
J. Polzehl, K. Tabelow. Structural adaptive smoothing in diffusion tensor imaging: The R package dti., Journal of Statistical Software 31, (2009).
J. Polzehl, K. Tabelow, Beyond the Gaussian model in diffussion-weighted imaging: The package dti, J. Statist. Software, 44, 1-26 (2011).
K. Tabelow, H.U. Voss, J. Polzehl, Modeling the orientation distribution function by mixtures of angular central Gaussian distributions, Journal of Neuroscience Methods 203(1) 200-211 (2012).
S. Becker, K. Tabelow, H.U. Voss, A. Anwander, R.M. Heidemann, J. Polzehl, Position-orientation adaptive smoothing of diffusion weighted magnetic resonance data (POAS), WIAS-Preprint No. 1668, (2011).

Download: CRAN, which may contain a newer version, or dti_0.9-0.tar.gz, or dti_0.9-0.zip

Adaptive Weights Smoothing in AMIRA™

We provide an adaptive weights smoothing function for AMIRA™. It is included in the ZIB-release (see there).

Adaptive Smoothing in SPM2

We have developed a toolbox for structural adaptive smoothing for SPM2 which implements the structure adaptive smoothing procedure for single subject fMRI data. Go to the home of this project for detailed information and download.