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How diagnose Crohn's for sure?

My son recently had a colonoscopy which resulted in a perforation of his colon by his doctor and resident.  He had immediate surgery to remove his entire colon, and now has an ileostomy.  He had a MRI that showed no evidence of Chron's disease, the pathologist who analyzed the colon said he thought the tissue look to have Chron's too.  Not sure what to believer, this is the same person who said he could not see / find the perforation.

Does anyone know if there is better test to determine if he has Crohn's?  They are concerned a J-Pouch is appropriate if he does have it.

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