Image Pixel Intensities

As you move the mouse pointer over the image, the slice number, position within the slice, and pixel intensity are shown at the bottom of the Image Display frame. See dimension display.

You can show statistics about the image in the Image Statistics window. Click on Image Stats under the View menu:

This brings up the Image Statistics frame, as shown below:

The Image Statistics frame shows:

A histogram of pixel intensities. If the image has a selected slice, then the histogram is for all pixels in the selected slice, otherwise it is for the pixels in the image.
Note: The histogram intensity range shown on the x-axis reflects the intensity range selected by the contrast-adjustment sliders. As you alter the image contrast, the histogram is adjusted so show intensities only within the displayed min./max. intensity range.
The slice number for which statistics are shown. If the image does not have a selected slice, then the text "None selected" appears.
The number of pixels in the image (or the selected slice) that have a non-zero intensity.
Note: The number shown is for all non-zero intensity pixels, not just for the pixels within the max./min. intensity range.
The volume of pixels in the image (or the selected slice) that have a non-zero intensity. If the slice is planar (i.e., the slice thickness is not defined) then the text "N/A" appears.
Note: The volume shown is for all non-zero intensity pixels, not just for the pixels within the max./min. intensity range.
The mean intensity of pixels in the image (or in the selected slice).
Note: The mean shown is for all pixels, not just for the pixels within the max./min. intensity range (but excluding pixels with zero intensity from the calculation).

If you select the Show normalised check box

, then the number of pixels on the y-axis is normalised so that the sum of all histogram y-values is equal to 1.0.

As the mouse is moved over the histogram graph, the intensity and number of pixels at the mouse location are shown at the bottom of the Image Statistics frame.

As the mouse is moved over the image, the intensity beneath the mouse is shown as an orange vertical line on the histogram.

Note: the colours used in this and other graphs are customisable.

For movies, the Image statistics for the visible slice is continuously updated as the movie steps through the frames.

Writing the Statistics to File

To write the image statistics to a file, choose Write under the File menu in the Image Statistics frame:

The formal specification of an image statistics file is given in the file formats section. An example of the format of the image statics written to disk is shown below:

      
# Image stats written "06 Mar 2006 17:10:44" by Operator ID="xinapse"
# Image source= "/home/xinapse/images/A.PATIENT._001_STUDY_1_SERIES_6"
# Slice: 25
# Number of non-zero pixels: 17932
# Volume of non-zero pixels: 51302.45 cu mm
# Mean pixel intensity: 109.32
# Visible histogram:
0.0	4760.0
1.0	201.0
2.0	105.0
3.0	77.0
...

The data intensity histogram is written in a tab-separated table with two columns: the first is the pixel intensity value, and the second is the number of pixels with that intensity. For normalised histograms, the sum of all the values in the second column is equal to 1.0.

Creating a PDF File of the Graph

To write the image statistics histogram to a PDF, choose

Export as
      PDF

under the File menu in the Image Statistics frame:

A File Chooser will now pop up for you to select a PDF file to write the histogram.

Click the button when you have finished with image statistics.

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