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Are these images in the same subject? If so, is the PD image distorted relative to the T1? Peace, Matt. -----Original Message----- From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf Of Miranda Nelson Sent: Thursday, November 13, 2008 10:54 AM To: [log in to unmask] Subject: [FSL] FNIRT Question Hello, As I understand, FNIRT currently is not designed to register images with different contrasts. However, I would like to test FNIRT to see how it would do in registering a T1 (1x1x1) image to a PD (1x1x2) image. I am not an expert on all of the options that one is able to specify when running this program. Any suggestions as to how to go about doing this, or specific command-line options/syntaxes that might be successful? Thanks in advance!