Software Packages that are currently available for download from the ANSIR Laboratory at Wake Forest University School of Medicine
The WFU_DICOMtk software package converts 3-D image volumes or 2-D images to DICOM format and optionally sends them to a PACS server. It may also serve as a DICOM image viewer. The scripts are written entirely in MATLAB. The images input for DICOM conversion may be either 3-D volumes readable by SPM or any 2-D images supported by MATLAB's imread function. The software was developed in the ANSIR Laboratory at the Wake Forest University School of Medicine.
Current Release: 1.0
MATLAB 6.5 or greater with the Image Processing Toolbox
SPM2 or SPM5
The WFU SPM5 Pipeline is a fully automated method for the processing of fMRI data using SPM. It is fully automated from the point of data acquisition at the MRI scanner. It incorporates tools for automated data transfer, archiving, real-time SPM5 batch script generation with distributed grid processing, automated error-recovery procedures, full data-provenance, email notifications, optional conversion back to DICOM (Digital Imaging and Communications in Medicine), and picture archiving and communications systems (PACS) insertion. The architecture allows for an infinite number of easily definable analyses that are fully automated from the point of acquisition.
Current Release: 1.0
MATLAB 7.3 or greater with the Image Processing Toolbox
Non-Stationary Cluster Extent Correction for SPM
This toolbox implements the random field theory (RFT) version of cluster size inference under non-stationarity .
Non-stationarity, or non-uniform smoothness, is a problem in cluster size inference of brain imaging data. This is because, under non-stationarity, clusters tend to be large in smooth areas and small in rough areas within the image data. Non-stationarity is particularly problematic in VBM (voxel-based morphometry) data, and a use of cluster p-values has been discouraged in analyses of such data .
A solution for this non-stationarity problem was proposed by Worsley et al , and has been implemented in the FMRISTAT package. Accounting for non-stationarity is important as it could lead to an erroneous outcome of a VBM analysis, as demonstrated in Moorhead et al . We have ported the function for non-stationary cluster size inference from FMRISTAT to SPM, so that it can interface with the SPM output.
. Hayasaka S, Phan K L, Liberzon I, Worsley K J & Nichols T E. Nonstationary cluster-size inference with random field and permutation methods. NeuroImage 22: 676-687 (2004)
. Ashburner J & Friston K J. Voxel-based morphometry --- the methods. NeuroImage 11: 805-821 (2000)
. Worsley K J, Andermann M, Koulis T, MacDonald D & Evans A C. Detecting changes in nonisotropic images. Human Brain Mapping 8: 98-101 (1999)
. Moorhead T W J, Job D E, Spencer M D, Whalley H C, Johnstone E C & Lawrie S M. Empirical comparison of maximal voxel and non-isotropic adjusted cluster extent results in a voxel-based morphometry study of comorbid learning disability with schizophrenia. NeuroImage 28: 544-552 (2005)
Adaptive Staircase Procedure for E-Prime
This package provides the framework for implementing a self-adapting staircase procedure within the E-Prime programming environment. Although staircases have been in use for decades, the few open-source examples currently available require a moderate degree of programming proficiency to integrate into a new experimental procedure.
Here, we provide an example developed within the E-Prime that can be easily copied or manipulated for almost any experimental paradigm. It is based on the simple 2-down/1-up method, with adjustable step sizes (if s\desired) and experimenter-definable parameters. See the accompanying documentation for more detailed information on its use.
Current Release: 1.2.1
Hairston, W.D. and Maldjian, J.A. (2008) An adaptive staircase procedure for the E-Prime programming environment. Computer Methods and Programs in Biomedicine, <<...>> doi:10.1016/j.cmpb.2008.08.003
Developed in E-Prime 1.2. Currently not tested for E.P 2.0 and higher.
Please read the LICENSE agreement. You will be asked to accept its terms before you can download the software.