Update:
I think the problem is in using FSL 6.0, in which the output file of the -meanvol option is created without the redundant “.nii” or “.nii.gz” suffix inside the file name, and this is not what MCFLIRT expects (according to the “_gen_outfilename” method in the MCFLIRT class definition under the preprocess.py file).
I will therefore uninstall FSL 6.0 and work with FSL 5.0 instead.
Best,
Roey