It appears that there is a bug in how Fiji is handling the getDirectory command.  

Starting on 11/22 macros using getDirectory would no longer allow user selection from the OS of the directory where image sets were placed.  The user prompt appears for the first call for a path but no user prompt appears for the second call.  Occasionally the second user prompt will appear but as soon as the trackpad is touched the script continues and a null error is thrown since no directory is chosen.

 Installation of the latest daily Fiji build (1.48h10) did not solve the problem nor did attempting to run a simple test macro in ImageJ alone.

Test macro for degugging:
//getDirectory test 
dir1 = getDirectory("Choose Directory 1");
dir2 = getDirectory("Choose Directory 2");
print(dir1);
print(dir2);

It seems that the problem is with Java but that is just a guess.  Any help would be most appreciated while I try to gin up a work around.

Thanks so much.

John

Information about your version of Java:

  os.arch => x86_64
  os.name => Mac OS X
  os.version => 10.9
  java.version => 1.6.0_65
  java.vendor => Apple Inc.
  java.runtime.name => Java(TM) SE Runtime Environment
  java.runtime.version => 1.6.0_65-b14-462-11M4609
  java.vm.name => Java HotSpot(TM) 64-Bit Server VM
  java.vm.version => 20.65-b04-462
  java.vm.vendor => Apple Inc.
  java.vm.info => mixed mode
  java.awt.graphicsenv => apple.awt.CGraphicsEnvironment
  java.specification.name => Java Platform API Specification
  java.specification.version => 1.6
  sun.cpu.endian => little
  sun.desktop => null
  file.separator => /

The up-to-date check says: CHECK_TURNED_OFF

Information relevant to JAVA_HOME related problems:

  JAVA_HOME is set to: null
  ij.dir => /Applications/Fiji/Fiji.app

Information about the version of each plugin:

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  a77cab39 20130904170815 scripts/importTrackMateTracks.m