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Screensize: 640 x 480 800 x 600 1024 x 768 1280 x 1024 UserName: Password: Format Mode: Basic  Help  Prompt  Format: Font Andale Mono Arial Arial Black Book Antiqua Century Gothic Comic Sans MS Courier New Georgia Impact Lucida Console Script MT Bold Stencil Tahoma Times New Roman Trebuchet MS Verdana   Size 1 2 3 4 5 6   Color Black Red Yellow Pink Green Orange Purple Blue Beige Brown Teal Navy Maroon LimeGreen Message: * HTML is OFF * Forum Code is ON Smilies [quote][i]Originally posted by lh115[/i] [br]Hi, I am trying to register the resting state scan of multiple subjects to MNI space. After motion correction and high-pass/low-pass filtering, I have tried to input subjects resting scans into the FLIRT linear registration tool. Using the FLIRT GUI creates the following command: flirt -in filtered.nii -ref MNI152_T1_2mm_brain -out filtered_reg.nii.gz -omat filtered_reg2.mat -bins 256 -cost corratio -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -dof 12 -interp trilinear This works well but registers only one volume of the functional data. When I use the ‘-applyxfm’ option, FLIRT registers all of the volumes, but the brain becomes off center and cut off. Am I using this command correctly for a 4D image? Would it be possible to use FEAT somehow for registration? I was under the impression that the filtered_func_data.nii.gz from a lower level FEAT is not registered to MNI space. Thanks, Lars [/quote]   Check here to include your profile signature. Check here to subscribe to this topic.