The name stands for "Spect, Pet, And Mri analysis" and was selected because it is the goofiest-sounding acronym that can be created using the titular words. Before the onslaught of junk email that made "spam" a household word, a fellow at a scientific conference pointed out that, coincidentally, there is a tinned meat product available in England that has a very similar name. Go figure.
SPAMALIZE has two main types of programs: (i) end-use applications (detailed below) that have specialized features unavailable in similar commercial or academic software, and (ii) "filtering" programs that serve mainly to pre-process data in preparation for subsequent analysis by other programs. These "filtering" programs let us easily (?!) convert data from the formats spewed out by our various imaging machines to the formats needed by the many different end-use image analysis programs we use.
Bear in mind that this is an image analysis program, so this web-site has the innate philosophy that a picture is worth at least 300 words! The most mature and sought-after applications include:
BrainMaker: 3D Region-of-Interest (ROI) drawing and analysis. ROIs can be drawn on axial, coronal, and sagittal views to create a 3D Volume-of-Interest (VOI). Editing in one view automatically updates the ROI in all other views. There are many tools for drawing, erasing, editing, and automated contour finding. There is also a suite of tools for segmentation, smoothing, edge-finding, and easily applying histogram information to aid in drawing ROIs. The VOIs can be saved and applied to other image volumes (such as PET) to extract the corresponding pixel information.
BrainSpinner: 3D interactive volume display. Several volumes can be displayed simultaneuosly in different ways and the entire mess can be rotated in real time using the mouse as a virtual trackball. Mesmerizing. For instance, a PET scan of a brain can be displayed in planar view, a MRI volume can be used to show the outline of the brain, and activated areas (e.g. from SPM analysis) can be displayed as colored clouds.
BrainSqueezer: Display and Coregistration for multiple image volumes simultaneously. Multiple image volumes can be loaded and displayed, limited only by the size of the images and your available computer memory. Best of all, the images do not have to be the same size! Contours based on the current Reference image are applied to the other images to aid in judging the alignment. The object image may be coregistered (shifted, rotated, and magnified in 3 cardinal dimensions) to match the spatial location of the reference image. There is also an ImageMath module to add, subtract, and multiply (or mask) one image volume by another, and the result can be displayed immediately.
Once you use this you'll wonder how you ever did without it!
FDG Quantitation Tool: Converts a PET FDG scan from a "raw" concentration image (microCi/ml) to a "quantitated" local Cerebral Metabolic Rate of glucose (lCMRglu, mg/min/100g) image using a measured blood Time-Activity Curve. GUI-based, displays TAC and images. This program allows the user to investigate various "what if" scenarios, like "what if the radioactivity counter had reported a more realistic value for blood sample 3?".
There is copious input and output checking of the data and the file system, and a log-file is produced detailing everything that happened. If the blood curve and image file are OK, the program can also just run unattended and write out the lCMRglu image files.
Patlak/Logan Plot Tool: Performs multiple-time graphical analysis (MTGA) on dynamic PET or SPECT data. This is an integrated tool that readsand displays image data, reads and plots blood time-activity curves, allows you to define a reference region for an input function, and lets you draw ROIs on one or more planes. You can easily switch between Patlak plots (for irreversibly bound tracers) and Logan plots (for reversibly bound tracers). You may either draw a ROI over a particular region using this tool, or read in a mask created with another tool such as BraionMaker. You can also create a parametric image volume showing the Patlak slope calculated through all of the voxels in your data set!
As for the FDG program, there is copious input and output checking of the data and ROIs, and a log-file is produced detailing everything that happened.
SPAMALIZE knows how to read the following file types:
SPAMALIZE can write the following file types:
Other file types are added as needed.
SPAMALIZE runs on the following platforms:
SPAMALIZE requires a current version of IDL (available from Research Systems, Inc.). The University of Wisconsin has a campus-wide license agreement for IDL which makes it extremely reasonable for on-campus users.
Availability:
SPAMALIZE is available free of charge to any academic user. It is currently used by 25-30 groups in North and South America, Europe, and Asia. For information on how to download it, contact the author, Terry Oakes, at oakes@psyphw.psych.wisc.edu. Spamalize is officially unsupported unless you have made prior arrangements with Terry. A mildly helpful installation manual is available.