I don’t pretend to be an expert on fMRI, but there have been a number of well done studies on fMRI and acupuncture.  Examples here and here.  One of the main results, in my assessment, is that one can differentiate sham from verum acupuncture by fMRI.  This is important and may help to delineate properties of verum acupuncture points.

PLoS One. 2012;7(6):e39342. Epub 2012 Jun 22.
Altered Small-World Efficiency of Brain Functional Networks in Acupuncture at ST36: A Functional MRI Study.
Liu B, Chen J, Wang J, Liu X, Duan X, Shang X, Long Y, Chen Z, Li X, Huang Y, He Y.
Department of Radiology, Guangdong Provincial Hospital of Traditional Chinese Medicine, Guangdong, China.

BACKGROUND:

Acupuncture in humans can produce clinical effects via the central nervous system. However, the neural substrates of acupuncture’s effects remain largely unknown.
RESULTS:

We utilized functional MRI to investigate the topological efficiency of brain functional networks in eighteen healthy young adults who were scanned before and after acupuncture at the ST36 acupoints (ACUP) and its sham point (SHAM). Whole-brain functional networks were constructed by thresholding temporal correlations matrices of ninety brain regions, followed by a graph theory-based analysis. We showed that brain functional networks exhibited small-world attributes (high local and global efficiency) regardless of the order of acupuncture and stimulus points, a finding compatible with previous studies of brain functional networks. Furthermore, the brain networks had increased local efficiency after ACUP stimulation but there were no significant differences after SHAM, indicating a specificity of acupuncture point in coordinating local information flow over the whole brain. ..
CONCLUSIONS:
Our results suggest that acupuncture modulates topological organization of whole-brain functional brain networks and the modulation has point specificity. These findings provide new insights into neuronal mechanism of acupuncture from the perspective of functional integration. Further studies would be interesting to apply network analysis approaches to study the effects of acupuncture treatments on brain disorders.