Support:Step-by-step COMKAT GUI Example

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The step-by-step tutorial for using COMKAT in parameter estimation.

Contents

Introduction

This is a tutorial for using COMKAT to estimate parameter with the data set of microPET rat study. We will load the input function from the excel file, load image and draw region of interest. Then we will estimate the parameters for the ROI(s) and save estimation results.

Download testing data

Please go to Download:Test images:microPET to download the rat data. It's a zip file so you will have to unzip it to a folder on your computer.

Download and install COMKAT

Please refer to Getting started with COMKAT for more details.

Run COMKAT GUI

Once you have downloaded, installed, set path for and validated COMKAT, you may start the COMKAT GUI by typing 'comkat' in MATLAB and hit enter. The COMKAT GUI will open up.
If you are running COMKAT under standalone mode,just double click the executable file and COMKAT GUI will open. By default you should see:

COMKAT GUI steps 1.png

Load kinetic model

COMKAT step 10.png

Press the drop-down list of 'Select a model from templates' and choose 'FDG 2-compartment model'.

You should see the COMKAT GUI as below after the model loaded.

COMKAT step 9.png

Load input function

Load the first file (Continuous counting)


COMKAT step2.png

Press 'Get Data from File'. Then you will see the Input Function GUI opened.

COMKAT step 3.png

Click 'Browse' and choose the excel file in the testing data set for input function.

COMKAT step 4.png

And you will see this window:

COMKAT step 5.png

Click the drop-down menu under 'Column' to choose the right column for time data.

COMKAT step 6.png

Click the drop-down menu under 'Column' to choose the right column for activity data.

COMKAT step 7.png

With the right choices of units and columns, you should see the figure below:

COMKAT step 8.png

Click OK to return to Input Function GUI. You should see that the GUI has the first part of input function loaded.

COMKAT step 11.png

Load the second file (Manual samples)

Press 'File 2' to get the 2nd file.

COMKAT step 12.png

Press 'Manual samples' under 'Excel worksheets' to switch to the second worksheet.

COMKAT step 13.png

Do the following changes to read the manual blood samples. And then hit 'OK' to return.

COMKAT step 14.png

You should then see the Input Function GUI as this.

COMKAT step 15.png

Under 'Interpolation' select 'linear interpolation'.

COMKAT step 16.png

And then hit 'Next'.

COMKAT step 17.png

Keep hitting next to get to the last page of Input Function GUI. Hit 'Return to COMKAT GUI'.

COMKAT step 18.png

On the COMKAT GUI, now you should see that the input function has been loaded.

COMKAT step 19.png

Load image



Press the icon for loading image data.

COMKAT step 20.png

Under 'File', select 'Load Image'

COMKAT step 21.png

Choose the .img file of rat data.

COMKAT step 22.png

After several seconds, a dialog will pop up and prompt you to specify web site personalization orientation. Simply choose '#0 Unknown' in this case.

COMKAT step 23.png

Images are successfully loaded into COMKAT Image Tool.

COMKAT step 24.png

Draw region of interest



Right-click on the image and choose 'Add new VOI'.

COMKAT step 25.png

Change color and VOI name if you wish.

COMKAT step 26.png

Draw a region on the brain.

COMKAT step 27.png

Click button to return to COMKAT GUI.

COMKAT step 28.png

In the dialog for converting units, select 'nCi to uCi'.

COMKAT step 29.png

Under 'Output Function' in COMKAT GUI, you should now see a figure like this:

COMKAT step 30.png

Estimate parameters



Press 'Estimate' to estimate parameters.

COMKAT step 31.png

Save results



Press 'Save to save results.

COMKAT step 32.png