Difference between revisions of "Download:COMKAT R3"

Revision as of 17:15, 5 February 2008

About COMKAT R3

COMKAT R3 is released in February 2008. It is the latest release of COMKAT.

System requirement

OS: Mac OS, Linux and Windows.
MATLAB: As the mex files are compiled under different versions of Matlab, COMKAT on different platforms requires different Matlab release.

Windows: Matlab 7 and above
PowerPC-based Mac OS: Matlab R14 sp1 and above
Intel-based Mac OS: Matlab 2007a and above
Linux: Matlab R14 and above

Download

Download COMKAT R3: [1] (NOTE: You must log in to download it.)

New features

1. More powerful COMKAT Image Tool: Enhanced image fusion, display, ROI and VOI tools, etc.

2. Input function estimation: Estimate input function from the heart images without blood samples.

3. Graphical methods such as Patlak, Gunn methods and more.

4. Fast DICOM loading: Compiled functions for loading DICOM images and headers that are about 10 times faster than Matlab built-in functions.

5. Complete support on Mac OS and Linux.

6. Various bug fixes that make COMKAT run more smoothly.

7. Supports more image formats such as Analyze and NIFTI.

Installation

1. Download COMKAT_R3.zip.

2. Unzip it to your computer.

3. Set up search path for COMKAT. You may do either of the following: (1) Open Matlab, run 'SetComkatPath.m' under the COMKAT root folder.
Or (2) You may set up the paths manually. First, open Matlab and go to File -> Set Path. Click 'Add folder' and select the following folders. (COMKATROOT indicates a generic name for the folder that holds the COMKAT subfolders and files. For example, COMKAT_R3 might be an example of the root folder used for release 3.)

COMKATROOT/

COMKATROOT/comkat_GUI

COMKATROOT/ComkatImageTool

COMKATROOT/utilities

COMKATROOT/validation

After that, click 'Add subfolders' and select COMKATROOT/ImageReadingFunctions.

Within the MATLAB File -> Set Path tool you might need to use "Move Up" and "Move Down" to get the folders into the preferred order given above.

4. In MATLAB, execute command 'validate'. Validation Suite should pop up and allow you to select various computations to perform. The generated results are shown in a report displayed in a Web browser. Pay particular attention to the Results section of the report and compare new results generated on Your Computer (to the left) to ones previously generated on a COMKAT Developer's Computer (to the right) and deemed to be correct. Note that minor differences are expected due to finite numeric precision obtained with computers.

NOTE Mac users: To display tables in the COMKAT GUI properly, you have to set up your Matlab startup option to show Java elements by following these steps:

Find file named "Matlab" under Matlab_root/bin/mac (Matlab_root is your Matlab directory)
Press "ctrl" and click on the file "Matlab" (at the same time)
Select "Show Package Contents"
Another finder window should popup showing "Contents", enter this folder
Find a file named " launch_matlab.sh"
Open this file by TextEdit or any other editor
Modify the following line: $SHELL -c 'bin/mac/setsid bin/matlab -desktop -display :0.0 &' to $SHELL -c 'bin/mac/setsid bin/matlab -useJavaGUI -desktop -display :0.0 &'
Save "launch_matlab.sh"

@@ Line 5: / Line 5: @@
 == System requirement ==
 OS: Mac OS, Linux and Windows.
-<br>Matlab: As the mex files are compiled under different versions of Matlab, COMKAT on different platforms requires different Matlab release.
+<br>MATLAB: As the mex files are compiled under different versions of Matlab, COMKAT on different platforms requires different Matlab release.
 *Windows: Matlab 7 and above
@@ Line 40: / Line 40: @@
 (1) Open Matlab, run 'SetComkatPath.m' under the COMKAT root folder.
 <br>'''Or'''
-(2) You may set up the paths manually. First, open Matlab and go to File -> Set Path. Click 'Add folder' and select the following folders. (COMKATROOT is the root folder that you unzip COMKAT files under.)
+(2) You may set up the paths manually. First, open Matlab and go to File -> Set Path. Click 'Add folder' and select the following folders. (''COMKATROOT'' indicates a generic name for the folder that holds the COMKAT subfolders and files.  For example, COMKAT_R3 might be an example of the root folder used for release 3.)
-COMKATROOT/
+''COMKATROOT''/
-COMKATROOT/comkat_GUI
+''COMKATROOT''/comkat_GUI
-COMKATROOT/ComkatImageTool
+''COMKATROOT''/ComkatImageTool
-COMKATROOT/utilities
+''COMKATROOT''/utilities
-COMKATROOT/validation
+''COMKATROOT''/validation
-After that, click 'Add subfolders' and select COMKATROOT/ImageReadingFunctions.
+After that, click 'Add subfolders' and select ''COMKATROOT''/ImageReadingFunctions.
-. In Matlab, execute command 'validate'. Validation suite should pop up and
+''Within the MATLAB File -> Set Path tool you might need to use "Move Up" and "Move Down" to get the folders into the preferred order given above.''
-allow you to examine if results are correctly generated on your computer.
+. In MATLAB, execute command 'validate'. '''Validation Suite''' should pop up and
+allow you to select various computations to perform.  The generated results are shown in a report displayed in a Web browser.  Pay particular attention to the Results section of the report and compare new results generated on ''Your Computer'' (to the left) to ones previously generated on a COMKAT ''Developer's Computer'' (to the right) and deemed to be correct.  Note that minor differences are expected due to finite numeric precision obtained with computers.
 '''NOTE Mac users''': To display tables in the COMKAT GUI properly, you have to set up your Matlab startup option to show Java elements by following these steps: