Difference between revisions of "Download:COMKAT R3"

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== Download ==
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Click [http://comkat.case.edu/img_auth.php/comkat_software_download/COMKAT_R3.zip here] to download COMKAT R3. '''NOTE:''' You must [http://comkat.case.edu/index.php?title=Special:Userlogin&returnto=Download:COMKAT_R3 log in] first to download.
 +
 
== About COMKAT R3 ==
 
== About COMKAT R3 ==
  
−
COMKAT R3 is released in January 2008. It is the latest release of COMKAT.  
+
COMKAT R3 is released in February 2008. It is the latest release of COMKAT.  
  
 
== System requirement ==
 
== System requirement ==
 
OS: Mac OS, Linux and Windows.
 
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.  
−
 
 
−
*On Windows: Matlab 7 and above
 
−
*On PowerPC-based Mac OS: Matlab R14 sp1 and above
 
−
*On Intel-based Mac OS: Matlab 2007a and above
 
−
*On Linux: Matlab R14 and above
 
  
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== Download ==
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*Windows: MATLAB 7 (R14) and above
 +
*Windows 64-bit: MATLAB 2007b and above
 +
*PowerPC-based Mac OS: MATLAB R14 sp1 and above
 +
*Intel-based Mac OS: MATLAB 2007b and above
 +
*Linux: MATLAB 7 (R14) and above
 +
*Linux 64-bit: MATLAB 2007b and above
  
 +
NOTE: COMKAT supports 64-bit systems now.
  
 
== New features ==
 
== New features ==
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3. Graphical methods such as Patlak, Gunn methods and more.
 
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.
+
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.  
 
5. Complete support on Mac OS and Linux.  
Line 30: Line 34:
  
 
7. Supports more image formats such as Analyze and NIFTI.
 
7. Supports more image formats such as Analyze and NIFTI.
 +
 +
8. Supports 64-bit Matlab on Windows and Linux now.
 +
 +
== Installation ==
 +
 +
To install COMKAT to your system, follow these steps.
 +
 +
1. Download COMKAT_R3.zip from http://comkat.case.edu
 +
 +
2. Unzip it to your computer.
 +
 +
3. Set up search path for COMKAT. You may do '''either''' of the following:
 +
 +
(1) Automatic: Open MATLAB, run 'SetComkatPath.m' under the COMKAT root folder.
 +
 +
(2) Manual: 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.)
 +
 +
''COMKATROOT''/
 +
 +
''COMKATROOT''/comkat_GUI
 +
 +
''COMKATROOT''/ComkatImageTool
 +
 +
''COMKATROOT''/utilities
 +
 +
''COMKATROOT''/validation
 +
 +
After that, click 'Add subfolders' and select ''COMKATROOT''/ImageReadingFunctions.
 +
 +
4. Re-start MATLAB. Go to "File -> Set Path". Check if the COMKAT folders are in the paths. If not, that means you do not have the 'owner' access to a file called "pathdef.m" on your system. To solve this, type 'which pathdef.m' in MATLAB. It will show the location of this file. Ask your system administrator to give you write access to this file, and then set the path again.
 +
 +
5. In MATLAB, execute command 'validate'. Validation suite should pop up and allow you to examine if results are correctly generated on your computer.
 +
 +
6. If you are having trouble running the validation suite associated with'pxEval' or 'cvodesGenmod5' functions, that means you have a compatibility issue with these mex function. It's either that your MATLAB version is older than the one we used to compile these mex functions, or your platform is not supported by COMKAT yet. You may use the makefile to re-compile these mex functions again. Run the script 'makefile.m' under COMKAT root folder. Please contact us if you are having trouble running it.
 +
 +
NOTE: If you are running MATLAB versions before R2006, we strongly recommend you to re-compile the mex functions again to ensure every function is working properly.
 +
 +
''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''': For some older versions of MATLAB 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: ''<nowiki>$SHELL -c 'bin/mac/setsid bin/matlab -desktop -display :0.0 &'</nowiki>'' to ''<nowiki>$SHELL -c 'bin/mac/setsid bin/matlab -useJavaGUI -desktop -display :0.0 &'</nowiki>''
 +
#Save "launch_matlab.sh"
 +
 +
'''NOTE 64-bit Windows users''': When you install 64-bit MATLAB, it does not automatically install the Visual C re-distributable for you. But for 32-bit MATLAB it does. Since we compiled our mex files using Visual Studio 2008 for Windows, you will have to install the Visual Studio 2008 re-distributable in order to run the mex files. Otherwise you may get a mex file error. <br>Please go to Microsoft website: http://www.microsoft.com/downloads/details.aspx?familyid=bd2a6171-e2d6-4230-b809-9a8d7548c1b6&displaylang=en to download and install the re-distributables. If the link is broken, google '''Microsoft Visual C++ 2008 Redistributable Package x64'''.

Latest revision as of 20:42, 20 April 2012

Download

Click here to download COMKAT R3. NOTE: You must log in first to download.

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 (R14) and above
  • Windows 64-bit: MATLAB 2007b and above
  • PowerPC-based Mac OS: MATLAB R14 sp1 and above
  • Intel-based Mac OS: MATLAB 2007b and above
  • Linux: MATLAB 7 (R14) and above
  • Linux 64-bit: MATLAB 2007b and above

NOTE: COMKAT supports 64-bit systems now.

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.

8. Supports 64-bit Matlab on Windows and Linux now.

Installation

To install COMKAT to your system, follow these steps.

1. Download COMKAT_R3.zip from http://comkat.case.edu

2. Unzip it to your computer.

3. Set up search path for COMKAT. You may do either of the following:

(1) Automatic: Open MATLAB, run 'SetComkatPath.m' under the COMKAT root folder.

(2) Manual: 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.)

COMKATROOT/

COMKATROOT/comkat_GUI

COMKATROOT/ComkatImageTool

COMKATROOT/utilities

COMKATROOT/validation

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

4. Re-start MATLAB. Go to "File -> Set Path". Check if the COMKAT folders are in the paths. If not, that means you do not have the 'owner' access to a file called "pathdef.m" on your system. To solve this, type 'which pathdef.m' in MATLAB. It will show the location of this file. Ask your system administrator to give you write access to this file, and then set the path again.

5. In MATLAB, execute command 'validate'. Validation suite should pop up and allow you to examine if results are correctly generated on your computer.

6. If you are having trouble running the validation suite associated with'pxEval' or 'cvodesGenmod5' functions, that means you have a compatibility issue with these mex function. It's either that your MATLAB version is older than the one we used to compile these mex functions, or your platform is not supported by COMKAT yet. You may use the makefile to re-compile these mex functions again. Run the script 'makefile.m' under COMKAT root folder. Please contact us if you are having trouble running it.

NOTE: If you are running MATLAB versions before R2006, we strongly recommend you to re-compile the mex functions again to ensure every function is working properly.

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: For some older versions of MATLAB 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:

  1. Find file named "Matlab" under Matlab_root/bin/mac (Matlab_root is your MATLAB directory)
  2. Press "ctrl" and click on the file "Matlab" (at the same time)
  3. Select "Show Package Contents"
  4. Another finder window should popup showing "Contents", enter this folder
  5. Find a file named " launch_matlab.sh"
  6. Open this file by TextEdit or any other editor
  7. 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 &'
  8. Save "launch_matlab.sh"

NOTE 64-bit Windows users: When you install 64-bit MATLAB, it does not automatically install the Visual C re-distributable for you. But for 32-bit MATLAB it does. Since we compiled our mex files using Visual Studio 2008 for Windows, you will have to install the Visual Studio 2008 re-distributable in order to run the mex files. Otherwise you may get a mex file error.
Please go to Microsoft website: http://www.microsoft.com/downloads/details.aspx?familyid=bd2a6171-e2d6-4230-b809-9a8d7548c1b6&displaylang=en to download and install the re-distributables. If the link is broken, google Microsoft Visual C++ 2008 Redistributable Package x64.

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