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Multi-image Analysis GUI
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Using Mango
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Introduction    Display    ROI    Statistics    Graphs    Image Calculator    Transforms    Image Filters    Surface Rendering    Volume Rendering    Additional Info   

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Additional Info

Special Features

Convert Overlays to Components
A thresholded overlay is usually made up of multiple non-connected regions. It is possible to isolate these into a set of clusters using the 'Find Overlay Clusters..' option in the Analysis Menu. For example, this processing is helpful to break up ICA components derived from a resting state fMRI study into separate components. A dialog window opens when this option is selected and automatically identifies the largest eight non-connected regions or clusters. The Statistics window is also automatically opened listing stats for the eight regions. The small right-pointing arrow in the dialog opens a menu with an option to convert the current cluster (one with blue crosshair inside) into an ROI using the current ROI color. Moving the crosshair to different clusters and changing the current ROI color will create up to eight ROIs, one for each of the eight clusters.

Create Logical Overlays
When more than one overlay is present it is helpful to color code their overlapping volumes. The 'Create Overlay Logicals..' option in the Analysis Menu does this. This option supports more than two overlays (each with a different color table) and the number of combinations is automatically set up and calculated. The statistics window is opened summarizing the results for the overlapping regions. To the right of each overlay's color icon in the dialog is a right arrow that opens a menu with options to get stats for the overlay and to convert the it to an ROI.

Add Parametric Overlay...
This option is in the Viewer's File Menu. It is used when the source image for overlaying has both positive and negative values such for z-score images. When selected the file dialog is opened and the user selects the image to overlay onto the current viewer. This option assigns two color tables to the overlay, one for negative values and one for positive values, which can be adjusted separately.

Load Online Overlay...
This option is in the Viewer's File Menu. It is used to load an image as an overlay using a URL for images archived at a web address.

Load Online ROI...
This option is the Viewer's File Menu. It is used to load ROIs using a URL that have been archived at a web address.

Simple How To...

Edit The Origin
The user can change the site to use as the origin within an image. The default location of the origin is the first column, first row, and first slice. The origin can be changed to match the column-row-slice of a specific landmark within an image. To determine where the origin is currently located press the 'o' key and the crosshair will be positioned there. If a different origin is desired used the mouse to navigate the crosshair to the desired location then select the 'Origin...' option in the Viewer's Edit Menu. A small dialog will open with the current col-row-slice origin near the top and the current col-row-slice crosshair position in the x-y-z textbox. Pressing OK sets the origin to the values in the x-y-z textbox. You can type in col-row-slice values for the origin if you know them. Save the image to make changes permanent.

Edit a Voxel Value
The 'Voxel...' option in the Viewer's Edit Menu provides a means to view a voxel's value at the location of the crosshair and to change it. We mostly use this option to set points outside the brain to track their movement when transformed or to track the change in resolution when filters are applied. Save the image to make changes permanent.

Enter Notes
The 'Notes...' option in the Viewer's Edit Menu is where comments specific to an image can be entered. Suggestions include project title, subject code, transforms applied, filtering done, etc. Do not place HIPPA restricted data here. Save the image to make changes permanent.

Update Display to Full Range
The max and min display setting used by others are generally saved in an image's header so that the next time the image is opened the user will view the image with the same settings. To set the max-min range to the full range of image values click the 'Update to Image Range' option in the Viewer's Edit Menu. Save the image to make changes permanent.

Review Image Header Information
Image header information is accessed using the 'Image Info option in the Viewer's File Menu. Two levels of information are provided as tabs in the dialog window opened with this option:

Summary
The summary information is a subset of the image header that formatted for easy reading (example in Figure 2). It includes the file name and location as well as key data that are needed to properly display images and make measurements.

Header
The information at the 'Header' tab is the native image header. The most extensive image header is that for DICOM images. For traditional multi-slice DICOM images each slice's data is in a different file with a different header. Mango has a next button to move to different slices; however, moving the crosshair to the slice of interest will also bring up the corresponding slice header. Since DICOM headers contain a great deal of text and data specific tags we provided an option to search this header info.