Software Tools

cardviews

Cardviews is a CARDinal plane VIEWing System developed at the Center for Morphometric Analysis at the Massachusetts General Hospital. It is a tool for brain morphometry (including volumetric analysis using xvol) and this program emerged as a product of our methodological development. While some of its functionality is specifically tailored for our general segmentation and neocortical parcellation routines, the imaging interface, segmentation tools, and localization capacity have utility extending beyond the specific aims motivating its initial conception. IATR Entry

SVV - Surface Volume Visualizer

SVV is an ITK-based visualization application that enables multiple anatomic regions to be visualized with independent control of surface features.

NVM - Developed by Neuromorphometrics, Inc., in conjunction with CMA

"NVM" is an open-source software tool for making precise quantitative neuroanatomical measurements in volumetric image data. It is the most recent incarnation of software that has been used since the mid '80s at Massachusetts General Hospital's Center for Morphometric Analysis to analyze coronal T1-weighted magnetic resonance brain scans. NVM is being freely released for non-commercial use so that researchers can focus on developing new abilities instead of re-inventing the basic platform. Basic features include the abilities to: load 3D image data in a variety of formats, crop and reslice scans into a normalized orientation, adjust image brightness and contrast, display data as single or multiple slices in sagittal, axial, coronal, and arbitrary oblique views with arbitrary zoom factors, and produce outlines around labeled brain regions using isointensity contours and manual drawing, and to log all user actions. IATR Entry

WebParc

‘WebParc’ is an effort to bring a clinically efficatious means for the quantitative localization of lesion (principally stroke) in the hospital on the clinical floor. This requires transparent and secure image data transfer from clinical Radiology PACS to the processing station, efficient, expert clinician-suided lesion identification, and relatively precise localization. The target is to have these functions delivered in under 10 minutes. This effort represents the transitioning high anatomic resolution interpretation into the clinical environment

Brain Atlas for Functional Neuroimaging (BAFI) - Distributed by Theime Medical Publishers

This is a CD ROM Product distributed by Theime Medical Publishers. It supports a complete electronic version of the Talairach Atlas, as well as gyral-level description of the human brain. In addition, this tool permits the incorporation of user image data, both structural and functional, into the viewer for direct co-visualization with the atlas. IATR Entry

fmri_stattool

A tool for performing statistical analysis of fMRI time domain data. This work introduces the use of a curve evolution approach that provides separate estimates of the response time shifts at each phase of the stimulus on a pixel-by-pixel basis. This also implements a robust hypothesis test based on a Laplacian noise model. Download

diffusion_smoothing_tool

This tool implements a unified approach to variational smoothing and segmentation to brain diffusion tensor image data along user-selected attributes derived from the tensor, with the aim of extracting detailed brain structure information.  The application of this framework simultaneously segments and denoises to produce edges and smoothed regions within the white matter of the brain that are relatively homogeneous with respect to the diffusion tensor attributes of choice. IATR Entry Download

2D_skeletonization_tool

A 2D shape skeletonization tool. Download

3D_skeletonization_tool

A 3D shape skeletonization tool. Download

2D_shape_skeleton_comparitor

A 2D shape skeletonization comparison tool. Download

real-time_ITK_level-set_segmentor

We have developed a real time approach for discrete implementation of the level-set segmentation method. Download

FreeSurfer - Priors for Automated Segmentation Developed by CMA

FreeSurfer is a set of semi-automated tools for reconstruction of the brain's cortical surface and overlay of functional data onto the reconstructed surface. IATR Entry