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 BIAC MATLAB Tools 3.1.0 in testing

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T O P I C    R E V I E W
syam.gadde Posted - Sep 19 2006 : 3:27:07 PM
The next release of the BIAC MATLAB Tools is available for testing. It is installed in:
  • \\gall\programs\User_Scripts\BIAC_matlab_ver3.1.0_test
The easiest way to test this is to create a shortcut to MATLAB on your desktop, right-click on it and select "Properties", go to the "Shortcut" tab, and enter the above directory to the "Start in" box. The appropriate paths will then be automatically added when you start MATLAB from that shortcut. Alternatively, you can run the following commands when starting MATLAB:
addpath \\gall\programs\User_Scripts\BIAC_matlab_ver3.1.0_test\mr
addpath \\gall\programs\User_Scripts\BIAC_matlab_ver3.1.0_test\general
Many of the updates have been available in User_Scripts\beta for a while, so many of you may already be using some of the new functionality. However, new versions of readxml are not backwards-compatible with older versions of readmr, necessitating a minor version number bump to 3.1. The included .mex files will only work with MATLAB 7 on Windows machines, MATLAB 6.5 or 7 on Linux, or MATLAB 6.5 on AIX (e.g. golgi). Other versions/environments will require re-compilation of the .mex files using buildmex.m, buildmex.bat or buildmex.sh.

These tools will be in a testing phase for several weeks before being installed in the standard locations. I encourage you to test this release and report any problems by replying to this topic.

Important updates:
  • Native NIfTI-1 and compressed NIfTI-1 support in readmr and support for compressed NIfTI-1 data wrapped with BXH headers (reading compressed data only works reliably with MATLAB 7 due to Java issues)
  • Native MATLAB (non-compiled non-.mex) versions of readxml and writexml are provided for use when the compiled versions are unavailable. They are very slow.
  • Data wrapped with XCEDE (BIRN's XML format, based on the BXH format) files are supported by readmr.
  • showsrs2 now displays RAS/LPI labels at edges of images if this information is available in the image headers.
  • showsrs2 supports a new flag 'DELAYINTERP' to help save memory when loading large datasets
  • showsrs2 now supports 2D clustering
  • Many bug fixes and much code cleanup.
3   L A T E S T    R E P L I E S    (Newest First)
syam.gadde Posted - Dec 06 2006 : 2:20:25 PM
Due to some unexpected complications with the upgrade (apparently everyone may need to exit any MATLAB process that uses the standard MATLAB BIAC directory), this has been postponed to Monday, Dec. 11 at 5PM. I encourage BIAC users to exit any interactive MATLAB sessions that use the standard BIAC MATLAB directories by 5PM Monday. The upgrade downtime should be minimal, and the change should be mostly transparent, especially for those who have tested the new versions of the tools. If there are any concerns with the timing of this upgrade, please post here.
syam.gadde Posted - Nov 17 2006 : 4:04:49 PM
We are planning the switch over to version 3.1.0 of the BIAC matlab tools the week of November 27. This version adds many nice features and bug fixes to the currently installed version of the tools. Please test your programs before then to minimize any potential problems. You can see the change log in the VersionHistory.txt file in the test directory (listed above).
syam.gadde Posted - Sep 20 2006 : 10:54:41 AM
You can also test this on golgi by doing the following:
mkdir -p ~/matlab
cp ~/net/gall/programs/User_Scripts/BIAC_matlab_ver3.1.0_test/startup-stub.m ~/matlab/startup.m
This will make sure the standard BIAC tool directories are added to your MATLAB path when you start up MATLAB. To use the new "test" version of the tools do the following before starting MATLAB:
export BIACMATLABROOT=/home/gadde/net/gall/programs/User_Scripts/BIAC_matlab_ver3.1.0_test
export MATLAB_JAVA=/usr/java14/jre
If you want these command sto be run every time you login, add them to your ~/.profile file, using either nedit or xemacs.
Lastly, you need to run matlab like this to get Java working:
matlab -jvm
Then the new version of tools should be fully available to you. (After the testing phase, the export commands will be integrated into the standard login and -nojvm will be taken out of the standard matlab script so just typing "matlab" will be sufficient.)

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