Difference between revisions of "Support:Step-by-step COMKAT GUI Example"

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== Load input function ==
 
== Load input function ==
 
[[Image:COMKAT step2.png]]
 
[[Image:COMKAT step2.png]]
Press 'Get Data from File'. Then you will see the Input Function GUI opened.
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<br>Press 'Get Data from File'. Then you will see the Input Function GUI opened.
 
[[Image:COMKAT step 3.png]]
 
[[Image:COMKAT step 3.png]]
Click 'Browse' and choose the excel file in the testing data set for input function.  
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<br>Click 'Browse' and choose the excel file in the testing data set for input function.  
 
[[Image:COMKAT step 4.png]]
 
[[Image:COMKAT step 4.png]]
 +
<br>And you will see this window:
 +
[[Image:COMKAT step 5.png]]
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[[Image:COMKAT step 6.png]]
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[[Image:COMKAT step 7.png]]
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[[Image:COMKAT step 8.png]]
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[[Image:COMKAT step 11.png]]
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[[Image:COMKAT step 12.png]]
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[[Image:COMKAT step 13.png]]
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[[Image:COMKAT step 14.png]]
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[[Image:COMKAT step 15.png]]
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[[Image:COMKAT step 16.png]]
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[[Image:COMKAT step 17.png]]
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[[Image:COMKAT step 18.png]]
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[[Image:COMKAT step 19.png]]
  
Select 3rd column as the activity, use 'micro Ci/ml' as unit. Hit 'OK'.
+
<br>Select 3rd column as the activity, use 'micro Ci/ml' as unit. Hit 'OK'.
  
Press 'File 2', hit 'Browse' again. Select the same excel file. Switch to the 'manual samples' worksheet.
 
  
Do the following changes:
+
<br>Press 'File 2', hit 'Browse' again. Select the same excel file. Switch to the 'manual samples' worksheet.  
 
 
Use 'linear interpolation'.  
 
  
  
 +
<br>Do the following changes:
  
 +
Use 'linear interpolation'.
  
  
 
== Load image ==
 
== Load image ==
 +
[[Image:COMKAT step 20.png]]
 +
[[Image:COMKAT step 21.png]]
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[[Image:COMKAT step 22.png]]
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[[Image:COMKAT step 23.png]]
 +
[[Image:COMKAT step 24.png]]
  
 
== Draw region of interest ==
 
== Draw region of interest ==
 
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[[Image:COMKAT step 25.png]]
== Adjust parameter estimation settings ==
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[[Image:COMKAT step 26.png]]
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[[Image:COMKAT step 27.png]]
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[[Image:COMKAT step 28.png]]
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[[Image:COMKAT step 29.png]]
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[[Image:COMKAT step 30.png]]
  
 
== Estimate parameters ==
 
== Estimate parameters ==
 +
[[Image:COMKAT step 31.png]]
  
 
== Save results ==
 
== Save results ==
 +
[[Image:COMKAT step 32.png]]

Revision as of 22:36, 13 April 2009

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

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 being loaded. COMKAT step 9.png

Load input function

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 COMKAT step 6.png COMKAT step 7.png COMKAT step 8.png COMKAT step 11.png COMKAT step 12.png COMKAT step 13.png COMKAT step 14.png COMKAT step 15.png COMKAT step 16.png COMKAT step 17.png COMKAT step 18.png COMKAT step 19.png


Select 3rd column as the activity, use 'micro Ci/ml' as unit. Hit 'OK'.



Press 'File 2', hit 'Browse' again. Select the same excel file. Switch to the 'manual samples' worksheet.



Do the following changes:

Use 'linear interpolation'.


Load image

COMKAT step 20.png COMKAT step 21.png COMKAT step 22.png COMKAT step 23.png COMKAT step 24.png

Draw region of interest

COMKAT step 25.png COMKAT step 26.png COMKAT step 27.png COMKAT step 28.png COMKAT step 29.png COMKAT step 30.png

Estimate parameters

COMKAT step 31.png

Save results

COMKAT step 32.png