MEDx 3.4.x Features

For a summary of the comprehensive and powerful feature set provided by MEDx, see our handy features-at-a-glance chart.

SPM-99

Over the last year, the incorporation of SPM-99 into MEDx has been our most-requested new feature. We're happy to announce that we have built an executable version of SPM-99 that will be distributed with MEDx 3.4. This version of SPM-99 will be started from a menu withing MEDx, and will have the same look and feel as the interpreted Matlab version. It will not require a Matlab license to run; it will, however, require a valid MEDx 3.4 or higher license.

FSL 1.2

This new module is a collection of functional and structural brain image analysis tools developed by the Image Analysis Group at Oxford University under the leadership of Dr. Stephen Smith. The structural tools consist of an automatic brain extraction tool (BET), a Linear Registration Tool (FLIRT), and a noise reduction technique based on Smallest Univalue Segment Assimilating Nucleus (SUSAN). The Easy Analysis Tool (FEAT) provides an easy-to-use interface for the fMRI data analysis process. This interface enables the user to specify pre-processing steps such as motion correction, spatial filtering, global intensity normalization, and temporal filtering. The user can also specify a paradigm and the statistical method for individual or group analyses. The functional analyses employ a General Linear Model and a model-free approach for cases where no a priori knowledge of the expected response exists. FSL also includes tools for analyzing event-related fMRI experiments. The FSL module provides a powerful, fast, and robust alternative set of tools that complement and enhance the existing MEDx tool set.

ABLe

This module (Analysis of Brain Lesions) is used to characterize brain lesions in MR and CT images of the adult human brain. The module can be used to perform spatial operations such as: measuring lesion volume; spatially normalizing the lesioned brain into Talairach space; reporting qualitative and quantitative measures of registration accuracy; and reporting anatomic structures in the normalized brain using an interface to the Talairach Daemon. ABLe can also quantify Brodmann area involvement of the lesion based on the Damasio Atlas, simultaneously display groups of lesions across subjects, and quantify areas of overlap. ABLe was created in collaboration with the Cognitive Neuroscience Group at the National Institute on Neurologic Disorders and Stroke at the United States National Institutes of Health.

Functional Data Simulator

For researchers who are interested in probing the analysis algorithms in MEDx or elsewhere, we now offer a powerful functional data simulator. The simulator is a highly interactive and intuitive graphical tool for constructing realistic curves of signal intensity vs. time at a single pixel and then extrapolating to volumetric data. Users can create 4-dimensional data sets in MEDx with known parameters and then run these data through an analysis to gauge the effect on their CBV, CBF and MTT maps of noise, delay, or curve shape. The 4D data simulator can also be used to create synthetic fMRI data for similar exploration of the effects of noise, timing, etc., on the results of that technique.

No More Add-On Module Pricing!

Note that each of these features, including the Perfusion module, will be part of the MEDx base license; there will be no additional cost for any of these modules.

MEDx 3.3 Features

Complete Brain Perfusion Analysis Package

Now you can create CBV, CBF & MTT maps directly from your raw EPI data using one or more established algorithms. All steps from pre-processing (e.g., eliminating non-brain pixels) through map-making to post-processing (e.g., automated tissue segmentation) are contained in one easy-to-use feature. Many of these methods use gamma-variate fitting of the 'first pass response' at every pixel and numerical deconvolution of the input tissue curve to find the Residue function. A difficult aspect of quantitative perfusion analysis - identifying the arterial input function - has been significantly streamlined. Our crack staff has developed new methods for automatically and semi-automatically identifying arterial voxels. Arterial input functions (AIFs) can be constructed by the novice user or edited conveniently by the expert. An 'open' program design gives the advanced user the ability to change underlying algorithm parameters and the opportunity to monitor the processing of temporal data at all stages of the analysis. The package produces as many as 21 parametric maps from an individual data set as well as an html style report of the results and all the critical settings. For more detailed information, see our Perfusion page.

Interactive Brain Lesion Analysis

Segment brain lesions; overlay lesion region on an atlas of Brodmann areas; calculate degree of involvement of each cognitive area. Easy to use Brain Lesion 'Wizard' and informative demo guide user through this new feature. For more detailed explanation please see our Brain Lesion page.

MR Parameter Estimation

Calculate T1 estimates from your inversion recovery or saturation recovery data. Estimate T2 from multi-echo data. Make ADC maps. Use these easy-to-create maps for precise segmentation of tissue types or for monitoring changes in tissue structure. Demo script included in new release. For more detailed explanation please see the MR Parameters page.

Save as DICOM/DICOM

Send MEDx can now be used for converting a single slice, a single volume, or a group of volumes in MEDx to the widely accepted DICOM (MR, CT, or CR) format by using the new MEDx feature called Save As DICOM. During this conversion, the MEDx user can specify the values of many DICOM keys being written into the headers of the DICOM data. The DICOM data created by MEDx can then be sent by the new DICOM Send feature in MEDx via the DICOM protocol over the network to an external DICOM application, such as a medical scanner, an image archive system such as a PACS, the DICOM Receive window in a second MEDx session, etc. The new DICOM Send feature in MEDx can be used to also send DICOM data imported into MEDx by pre-existing DICOM features in MEDx called DICOM Query/Retrieve and DICOM Receive. Please see the DICOM pages of the MEDx web site for more information about all the DICOM features in MEDx.

Estimation of Spatial Smoothness

Be sure to properly apply the critical threshold to your Z-maps. Now you can use an improved method for calculating the degrees of freedom in your data by first calculating the spatial smoothness (i.e. 'resel' volume) of your images.

Interactive Talairach Daemon Interface

Access the popular internet tool developed by Jack L. Lancaster and colleagues at University of Texas for identifying the structural location of an activation site according to its Talairach coordinates. And, you never have to exit MEDx to do it! (Available for IRIX and Solaris).

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