Welcome to scan:STAT!

In this online documentation, you will find:

  1. A general description, list of features, and system requirements
  2. A description of each menu item
  3. A walkthrough, demonstrating some of the various features of scan:STAT.
  4. A troubleshooting guide
  5. Information about the sample images included with this release
  6. Credits and contact information

There is a website devoted to scanSTAT, which includes the most recent version of the documentation and download information. You can find it at:



Section 1: General description

scanSTAT is a data analysis and viewing software tool for medical imaging. It is intended to be a stand-alone application, able to perform tasks from simple image viewing to full statistical image analysis and presentation. In addition, scanSTAT is able to perform these tasks either on data already acquired and stored on disk or in real-time, as the data is acquired.

scanSTAT can:

Soon, scanSTAT will be able to:


System Requirements

Note: When you install scanSTAT, you must also place the file "scanSTAT Prefs" in the Preferences folder in your System Folder. scanSTAT will not run without this file. It is distributed along with the program.

Please don't give away copies of this program to other users. While we do intend it to be freely distributable, we'd like to keep track of who out there likes our work. Please refer any interested parties to the main scanSTAT web page, where they can download copies.


This is a development copy of the program and it may be very unstable. Not all menu items are functional, and the program cannot save images. We strongly recommend quitting all open applications and saving files before starting scanSTAT (it will crash). To date, we have not suffered any secondary data loss, such as damage to closed disk files.

Section 2: Menu Reference

The program has a very simple five menu structure: File, Edit, Statistics, Display, and Help.

The Apple Menu:

The only localized component of the Apple menu is the About box

File Menu:

This option selects between real-time and offline processing modes.
Process From File
This is the offline processing mode. When in this mode, the "Open Time Data..." function is used to select from saved MR files.

Real Time
In the real-time mode, when the user selects "Open Scanner for Data..." the program opens a socket connection to the MR scanner and begins importing live MR data as it is acquired. Obviously, this option cannot be enabled in demonstration versions of the code, as it requires the presence of a properly configured scanner. Configuration, however, is pretty easy. A small unix application on the scanner looks for the connection traffic and sends the images as needed.

Open Time Data...
This option opens up a Macintosh file selector dialog. Use this option to select a time-series of data for statistical processing (as opposed to just image review). Only when a file is opened with this selection can it be processed to seek areas of activation.

Select Base Image...
(not yet available) This option will allow you to import an arbitrary image onto which to overlay the statistical images that you create.

Define Paradigm
In order to perform statistical processing, you must have a paradigm reference vector. This defines the weighting to be given each image in the time series when creating any derivative statistics. scanSTAT supports the definition of the paradigm file in three ways:
Create by Key Press
(Not available in this version) In interactive real-time mode, the preferred way to create a pardigm file is by allowing the user (or subject) to indicate their state by pressing a button. We look at the Macintosh ADB port and track key presses on it. If "Use Key Press" is selected, the Key Press Prefs... dialog appears (see below).
Create with CProto
At this writing, Cproto, a paradigm file creator, exists standalone, rather than under this menu. You can run it by double clicking that application. CProto does the magic of computing the estimated brain response functions based on the paradigm timing. Use this option to create paradigm files offline.
Use File...
This opens the standard Macintosh File dialog. Here you can select a pre-existing paradigm file, typically created by CProto.
Key Press Prefs...
(not available in this version) In the interactive Real-time mode, it is necessary to specify a few user preferences, including the scan TR (so that the impulse response convolution selects the appropriate time base), and how to handle the keys. It will also prompt you to save the record of the subject's key presses. The save format is identical to the save format for the general paradigm files: a text list of the weights applied to each image.
View Image
This menu item is used to open images for simple review (as opposed to statistical processing). We presently support the import of analyze format, GE ".MR" format, and the MGH standards (bfloat, bshort, buchar). For the MGH style images, it may be necessary to change the byte swap flag (the last character in the header file) to manage these properly. We treat the value of "1" to mean "LittleEndian" and the value of "0" to mean BigEndian. Using this option on a data time-series brings up the first image in the series.

Start Calculation
Once the data time series has been opened and the paradigm chosen, this option starts the actual calculation of time series statistics.

Close the frontmost window

(not yet available) This will save the image in the active window in our local standard format, which allows for retrospective review of the overlays. The time series will not be saved.

Save As...
This is to be our image export function. It will be possible to save files as PICT, TIFF and for simple image files, GE and Analyze format. I will only add the MGH formats if truly pushed, as the header is too thin to make much use of it.

This will also allow image exporting in the abovementioned file formats.

Undo the last saved changes, reverting the file to its previous state.

Page Setup...
Print One
These are to be the usual printing dialogs.

Exit the program. A bug seems to keep us from quitting if no windows are open. You may experience this bug. If so, open any image file (using View Image, or Open Time Series...) and then quit.

Edit Menu

This menu contains the usual complement of cut copy and paste, mostly to support desk accessories at this time. In this version, the edit menu items are not useful, and will very likely cause the program to crash if used.

Statistics Menu

This menu allows you to determine various aspects of the statistical tests to be performed on a data time series.

Selects which of the tests listed below will be applied to the data time series.
Student's t-test
(not yet available) This test expects a paradigm file whose vector sum is 0. The two group t-test assumes that negative weightings are assigned to one group and positive weightings are assigned to the other. A special value (1234.5) describes images that are to be ignored in the analyses.

Pearson Correlation
Form maps of the correlation between the time history of intensity for each pixel and the reference vector. This is the primary output of fMRI Grinder.

(not yet available) This non-parametric statistic is used by some groups to find areas of activation. We don't use it at UCLA, but we will implement it in this program. Probably, though, not as a real-time statistic.

Global Normalization
When this option is selected, each image will first be normalized to have the same mean intensity as the first image in the series. This is reputed to correct for some problems of scanner drift.

Save Ratio File...
(not yet available) If using Global Normalization, this will save a text file showing the correction applied to each image.

Statistical Options
This brings up a dialog to select various prospective statistical options (those that require recalculation of the image series in order to see). These include Gaussian smoothing, the selected noise threshold, and the artifact detection options (see the tutorial section on artifact detection below ).

Display Menu

The display menu refers to changes in the way that images are displayed, but does not affect statistical calculations.

Always selected in this release. In a future version this will allow a toggle to a paged view in which each slice location fills a whole window (similar to NIH Image stacks)

Enable/Disable While-Calc Display
When selected, the color overlay indicating the results of the statistical calculations will be updated as each timepoint is added. This is the essence of the real-time imaging mode. However, it can also be used in offline processing, to observe how the statistical map evolves over time.

Size To
Magnification or minification of the image, from 1/4 size to eight times size. There are some bugs in this option--use with caution.

Show/Hide Color/Gray Bar
Places or removes a calibrated color or gray bar to the right of the currently displayed image. This indicates the values associated with each color or shade in the statistical overlay.

Time-intensity Graph
This item opens a time-intensity graph showing the timecourse of behavior in selected pixels. By default, it will show the activity in all pixels whose statistical values are above those selected below with "Overlay Options...". You may also select those pixels whose behavior will be plotted by clicking and dragging. See the walkthrough section on pixel selection and intensity for more information.

Show Range in T-I Graph
When selected, this option modifies the graph of intensity behavior over time to include the ranges of intensity of the selected pixels.

Show Artifact Data Graph
This option brings up a window displaying the data from the automated artifact detection routines. The details of the window are described in the walkthrough section on artifact detection.

View Options...
This is the window and level (Brightness and contrast) control for the gray scale images, which may be the entire contents of the window (if opened with View Image...) or the base image (in Overlay mode). You may also change the default interpolation mode for these images between bilinear and pixel replication. The sliders may or may not be operational in this version.

Overlay Options...
From here you have control over the appearance of the composite statistical and anatomical images. You may display either the raw statistic, the probability (actually the -log10 of the probability) or the slope (a parametric assessment of the magnitude of the MR signal change) or the slope thresholded by the statistical maps. You may also adjust the interpolation of the statistical images. Pixel interpolation is prefered, because it does not show the "statistics" for the imaginary interpolated pixels. You may find the view less pleasing, though. We can display only the positive, only the negative, or both the positive and negative statistical values. By definition, negative values all refer to pixels whose signal decreases when the reference paradigm increases.

Show Displacements( toggles to Show Pixel Increase/Decrease)
Selecting this menu option will change the bottom section of the Artifact Data Graph to the desired option. If you select Show Displacements, the window will show the pixel displacements for both cumulative and sequential traces. If you select Show Pixel Increase/Decrease, the graph will show the Increase/Decrease ratio, which gives somewhat different information. Both of these options are explained in the walkthrough section on artifact detection.

Show Motion Bullseye
This brings up the Motion Bullseye display, which can be used to track subject motion by plotting displacements in a center-of-mass calculation. The ranges of the display are set in the Statistical Options... menu item under Displacement. The functioning of this item is described in detail in a special subsection of the walkthrough section on artifact detection.

Utilities Menu

This menu supports access to the Header editing tools and will soon allow the creation of noise simulations.

Section 3: Walkthrough Demonstration

This version of scanSTAT is being distributed on a Macintosh-formatted CD with a number of sample data files. To install the program, just double click the compacted file to create a folder containing the primary application and a second folder containing the sample images. No INIT's, CDEV's or any changes at all are made within the system folder. However, a file called "scanSTAT Prefs" will appear along with the application. For the program to work, this file must be moved into the Preferences folder in your System Folder.

The Walkthrough

Each of the following sections is designed to illustrate a different feature set of scanSTAT. We recommend, however, that you do all of them sequentially in one sitting for maximum efficiency, as they are designed to work together.

Walkthrough Section 1: Viewing Images

Walkthrough Section 2: Processing an fMRI Time Series

Walkthrough Section 3: Changing Prospective Signal Parameters

Walkthrough Section 4: Adjusting the Statistical Overlay

Walkthrough Section 5: Selecting Pixels and Pixel Behavior

Walkthrough Section 6: Artifact Detection and Handling

Waljthrough Section 6B: Real-world artifacts

Walkthrough Section 7: Interactive Paradigm Creation

Background: Functional MRI
When magnetic resonance images (MRI's) of the brain are acquired in rapid succession they will show small differences in signal intensity in positions corresponding to focal areas of activation. These signal changes result from small differences in the magnetic resonance signal caused by variations in the oxygenation state of the venous vasculature. Using this non-invasive functional MRI (fMRI) method it is possible to localize functional brain activation in normal individuals with an accuracy of millimeters and a temporal resolution of seconds. Though numerous technical challenges remain, fMRI is increasingly becoming a key method in understanding the topographical organization of the human brain.

Generally, these activation maps are created by comparing the signal intensity fluctuations that occur in each pixel in a series of MR images, to a description of the behavioral activity or stimulus conditions. Following the terminology used at MGH, we call such desrciptions "Paradigm Vectors" or "Paradigm Files". The statistics describing the correlation of the brain signal and the paradigm file become the functional maps and are generally superimposed in color onto anatomical maps.

For more background information, you could check out a paper by Dr. Mark Cohen.

Section 4: Troubleshooting

Notes and Perversions:

If you have comments or questions, I would love to hear from you.

Section 5: About the Sample Images

The images are organized by file type, to demonstrate the program's ability to read a variety of formats. They are all found in the folder called "Standard Sample Data"

MGH Types

This is a 128*128 matrix multi-slice echo-planar image
Here you will find "small.bshort" a 75 image time series collected during visual stimulation. The file, "small.C.p" can be used as a paradigm file to calculate statistics
This 16 slice file shows activity during hand ("hand.p" and language "lang.p" tasks in a patient with a large brain tumor. The file "tongue.p" describes the activity in a different collection series and should thus be largely uncorrelated.

Signa Genesis format

Analyze Format

Section 6: Credits and Contact Info

scanSTAT was (and is being) written by Mark S. Cohen and William L. Scheding at UCLA's Brain mapping center. They can be reached at:

mscohen@ucla.edu (Mark Cohen) or wls@ucla.edu (William Scheding)

This documentation was created using GoLive CyberStudio 2.0.2 by Dr. Cohen and Richard DuBois.

©1998Mark S. Cohen