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----- Original Message ----- From: Anna Barnes To: Julian Henty Sent: Wednesday, March 04, 2009 1:38 PM Subject: please forward to FSL list for me and change subject heading to: FSLVBM image input Dear FSL users, I have just started using the FSLVBM tools and I need some clarification regarding image inputs. I've used fsl_vbm_bet1 -N to do the first level of processing on my MPRAGE images but on inspecting the results I find that the *_struc_cut.nii images have the LH side of the face removed and lots of neck remaining and the *_struc_brain.nii still having lots of neck left although most of the skull has been stripped. I assume that the first *struc_cut.nii step is suppose to remove most of the neck. The MPRAGE images are collected in sagittal orientation and FSLview displays them with all the correct orientation labels (A,P,S,I,L,R). Do I need to re-slice images into transaxial orientation before using the VBM scripts? thanks Anna -- Anna Barnes, PhD Research Associate (+441223 764676) Brain Mapping Unit (Sir William Hardy Bldg.) Dept. of Psychiatry. c/o Experimental Psychology University of Cambridge. Downing Site, Downing St. Cambridge, CB2 3EB