SpmFlirt - MRC CBU Imaging Wiki

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Using FLIRT to coregister EPI and structural

The software is installed at the CBU. For those outside the CBU, you will need the Oxford software bundle which includes a variety of versions of the Brain Extraction Tool (BET), and the image registration program FLIRT. These programs need to be on your executable path. You also need some matlab m files I wrote (bet.m flirt.m flirt_coreg.m), available via this Flirt http directory. These m files need to go on your matlab path.First, create a version of the structural image with the skull and scalp removed, using BET. Start SPM, and from the matlab prompt (>>), type


Select the structural image(s) to skull strip and let the program run. You now have skull stripped versions of the structural images prefixed with 'ss_'.To run the EPI -> structural coreg, go the the >> prompt in the matlab window, and type:


Select number of subjects, coregister only, then select the skull stripped structural image as the target, the mean EPI image as the object image, and as 'Other images', select the EPI time series (slice time corrected, after realignment) (a000*img usually). Choose Correlation ratio as the cost function, and 'RB zooms and shears (12)' for the 'Degrees of freedom'. Check the eventual output; thence you can normalize the structural and reslice the EPI images etc.You might consider using linear only normalization, or normalization with few nonlinear basis functions; the remaining imperfect match between the EPI and structural image means that the higher detail warps calculated for the structural may be applied to the wrong area of the functional.

Matthew Brett 26/10/00