Thanks. Here is what I did with the info:
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lissot.net]
3dMINCtoAFNI.sh [-f] [-d destDir] sourceDirs(s) sourceFile(s)
This is a GPL wrapper to 3dMINCtoAFNI. It takes any combination of minc files and directories as arguments. The directories are searched recursively for minc files. The resultant afni files are copied into a common directory. Most importantly, for my purposes anyway, it propagates the protocol field from the minc header into the afni header in the form of a note. The enterprising user could add other fields by following the example.
-Tony