Oh right, thanks Mark. I'm used to using AFNI tools that mostly rely on single minus options that don't require an equals sign. Thanks for the pointer to the proper syntax. It seems to be working now. Perhaps another reason I got confused is that oxford_asl does seem able to take a value for a double minus option without the equals sign, as in:
oxford_asl -i ASL_335_diff.nii.gz --tis 1.8 -s MPRAGE_sag_9min.nii.gz --structout --bolus 1.5
At least, if it isn't working I don't see an error. Probably having even a single usage example in the help would be, you know, helpful.
Anyway, thanks again for your help and the truly great software.
-Will
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