That's a tough one.
I found a study comparing the two. It's in kids but I think it's applicable.
I just read over your first post and as long as you're pricing tests, I suggest you price [wiki]fecal lactoferrin[/wiki], [wiki]fecal calprotectin[/wiki], and vitamin B12 levels.
Since it's the cheaper route, here's some more studies/papers on MRE you can Google to see if you'd be comfortable with it:
1. Ernst O, Asselah T, Cablan X. Breath-hold fast spin-echo MR imaging of Crohn's disease. AJR Am J Roentgenol. 1998;179:127–8. [PubMed]
2. Koh DM, Miao Y, Chinn RJ, Amin Z, Zeegen R, Westaby D, et al. MR imaging evaluation of the activity of Crohn's disease. AJR Am J Roentgenol. 2001;177:1325–32. [PubMed]
3. Low RN, Francis IR, Politoske DA, Benett M. Crohn's disease evaluation: Comparison of contrast-enhanced MR imaging and single-phase helical CT scanning. J Magn Reson Imaging. 2000;11:127–35. [PubMed]
4. Maccioni F, Viscido A, Broglia L, Marrollo M, Masciangelo R, Caprilli R, et al. Evaluation of Crohn disease activity with magnetic resonance imaging. Abdom Imaging. 2000;25:219–28. [PubMed]
5. Madsen SM, Thomsen HS, Munkholm P, Schlichting P, Davidsen B. Magnetic resonance imaging of Crohn disease: Early recognition of treatment response and relapse. Abdom Imaging. 1997;22:164–6. [PubMed]
6. Schunk K, Kern A, Oberholzer K, Kalden P, Mayer I, Orth T, et al. Hydro-MRI in Crohn's disease: Appraisal of disease activity. Invest Radiol. 2000;35:431–7. [PubMed]
7. Low RN, Sebrechts CP, Politoske DA, Bennett MT, Flores S, Snyder RJ, et al. Crohn disease with endoscopic correlation: Single shot fast spin-echo and gadolinium-enhanced fat-suppressed spoiled gradient-echo MR imaging. Radiology. 2002;222:652–60. [PubMed]
8. Laghi A, Borrelli O, Paolantonio P, Dito L, Buena de Mesquita M, Falconieri P, et al. Contrast enhanced magnetic resonance imaging of the terminal ileum in children with Crohn's disease. Gut. 2003;52:393–7. [PMC free article] [PubMed]
9. Schunk K. Small bowel magnetic resonance imaging for inflammatory bowel disease. Top Magn Reson Imaging. 2002;13:409–25. [PubMed]
10. Bernstein CN, Greenberg H, Boult I, Chubey S, Leblanc C, Ryner L. A prospective comparison of MRI versus small bowel follow through in recurrent Crohn's disease. Am J Gastroenterol. 2005;100:2493–502. [PubMed]
11. Schreyer AG, Geissler A, Albrich H, Schölmerich J, Feuerbach S, Rogler G, et al. Abdominal MRI after enteroclysis or with oral contrast in patients with suspected or proven Crohn's disease. Clin Gastroenterol Hepatol.
2004;2:491–7. [PubMed]
12. Umschaden HW, Szolar D, Gasser J, Umschaden M, Haselbach H. Small-bowel disease: Comparison of MR enteroclysis images with conventional enteroclysis and surgical findings. Radiology. 2000;215:717–25. [PubMed]