Not really a help request per se as I just figured out my own problem, but I'm leaving the solution here for posterity. I have already submitted a bug report with similar information to that below.

The ImageMagick programs contained within the BXH/XCEDE tools don't appear to work on current versions of Mac OS X (I'm on El Capitan here, but from my searches it appears that this bug would happen for any version >= 10.7 Lion). I ran into this using fmriqa_generate.pl but any other functions that use ImageMagick likely have the same problem.

Errors like this appear when invoking ImageMagick's 'convert' or 'montage' tools:
dyld: Library not loaded: /System/Library/Frameworks/OpenCL.framework/Versions/A/Libraries/libclparser.dylib
Referenced from: /Users/mjohnson113/Downloads/bxh_xcede_tools-1.11.1-MacOSX.i686/bin/convert
Reason: image not found

From web searches, I deduced that the .dylib in question doesn't seem to exist anymore in Lion and up.

I fixed the problem for myself by installing ImageMagick via MacPorts and replacing the 'montage' and 'convert' binaries in the BXH/XCEDE package with the freshly built copies from MacPorts. Not sure what the best long-term solution would be for the project.

Anyway, if you are having the same problem, installing your own copy of ImageMagick and replacing the broken BXH/XCEDE copies with custom-built ones should, in theory, work for you too!

Thanks for doing the grunt work, and providing detailed workarounds to these issues. I will likely get rid of the ImageMagick executables packaged with bxh_xcede_tools since the standard ImageMagick tools are stable enough now. In the past, ImageMagick behavior would change drastically from minor version to minor version, but now things are less volatile.

Sounds good! Yes, it seems reasonable to me to just have people install ImageMagick for themselves... MacPorts and Homebrew make that pretty easy even if you're not running Linux.