NVM

NVM is now available for Linux, Windows XP and Macintosh OS X:

Description:

"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 has been released with source code so that researchers can focus on developing new abilities instead of reinventing the basic platform.

NVM screen dump (click for larger image):

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 iso-intensity contours and manual drawing, and to log all user actions.

The outputs of NVM are named neuroanatomical regions represented as surfaces or outline files. The user selects from the following tools to interact with the scan: arrow (selection), contour, draw, nudge, erase, box, landmark, label, and histogram. Seven differently colored temporary "contours" can be created using the contour tool and these are edited using the drawing tool and eraser. A click with the contour tool causes iso-intensity contours to be drawn everywhere in the slice image at the intensity of the voxel under the mouse pointer during the click. After editing, contours are extracted (or converted) into "outlines".

The label tool allows a text label to be assigned to a particular outline. The landmark tool is used to designate locations in the scan that are used for cropping and positional normalization. The histogram tool brings up a window showing the histogram of a region defined by an outline and a click on the histogram will generate an iso-intensity contour. "Mid-Peak" ISO-intensity contours can be generated by clicking on one peak and dragging to another. The "AutoContour" feature associates a particular intensity value with a contour color so that when the user changes to a different slice, this contour is automatically drawn. The intensity used for a particular slice is interpolated from the values that were set in the nearest slices.

The most significant and novel feature is called "SegMentor". This provides on-line, context sensitive instructions, definitions, and assistance with segmentation methods using a collection of XML and HTML documents.

SegMentor records, plays, and allows viewing and editing of scripts. At the top level, these scripts are flexible lists of tasks to perform. At the lowest level, SegMentor scripts control NVM tools, provide short user reminders, and also provide context-sensitive information to the user via "Help" buttons/menu which open a browser window to a web page containing images and definitions that describes the specific segmentation task in detail.

SegMentor scripts can be created to provide an explicit and complete definition of a particular neuroanatomical measurement method. This is important because it is not possible or desirable to fit all of the details of a method into an academic publication. Developing neuroanatomical measurement methods using SegMentor facilitates the distribution of these methods and is also invaluable in training new people to perform these methods. Moreover, SegMentor helps to automate the method, which decreases cost and increases reliability. By automating segmentation as much as possible, user input is limited to only the steps that need to be done using experience and anatomical knowledge.

A SegMentor script, along with the ability to log all user actions, provides complete documentation that can be essential to demonstrating scientific validity and to survive an FDA audit.