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Hi, You should make 3 rows: X1 X2 X3 . Y1 Y2 Y3 . Z1 Z2 Z3 . Then run the DTI preprocessing up through DTIFIT. You can then load the FA and 2 V1 images in FSLView setting one to lines and the other to colors modulated by FA intensity. Then check to see that the lines flow smoothly and continuously in the corpus callosum in the coronal and axial planes, and the corona radiata in the sagittal plane. If you need to negate (or flip) one of the gradient directions, the diffusion lines will be 180 opposite of what they should be in 2 of the 3 planes. The plane that looks correct will not contain the dimension that needs to be flipped (e.g. the axial plane contains x and y dimensions, and not z, so if axial is correct and coronal and sagittal are not, then z would need to be negated). Peace, Matt. _____ From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf Of Christi Perkins Sent: Friday, September 07, 2007 12:21 PM To: [log in to unmask] Subject: [FSL] Gradient Table preparation Hello all, I am in the middle of processing DTI data from a 3T Philips magnet and have run into a problem creating my bvecs file. The gradient table below was taken directly from the magnet. 1,0,0 0,1,0 0,0,1 -0.1789,-0.1113,-0.9776 -0.0635,0.3767,-0.9242 0.7108,0.0516,-0.7015 0.6191,-0.4385,-0.6515 0.2424,0.7843,-0.571 -0.2589,-0.618,-0.7423 -0.8169,0.1697,-0.5513 -0.8438,0.5261,-0.106 -0.2626,0.9548,-0.1389 0.0001,0.9689,0.2476 0.7453,0.6663,0.0242 0.9726,0.2317,0.0209 0.,0.,0. I have read on this website (http://www.nottingham.ac.uk/radiology/paul/software/dti_processing.html) that you need to "negate the x and z components" before producing the bvecs file. I'm assuming this is because FSL operates in a different coordinate system than the Philips scanner. Could anyone give me information on whether or not I need to negate some part of this gradient? Are there any other alterations I need to make before creating my bvecs file? Thanks so much for any info you can give me Christi