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Hi I've just started using fsl and I currently have coronally acquired images that have been converted from dicom to analyze using mricro (256 124 256). The BET function appears to include alot of non-brain. I have tried to tune the parameters and change the image centre as suggested in previous emails. However I still get non-brain tissue in the extracted image. I want to do serial atrophy measure using siena and don't know how this will affect the output measure. I was thinking of manually editing the bet images and then running the siena script. Is this possible? if so which images from bet do I need to edit and which lines in the siena script do I need to comment out? I presume to run the siena script I enter the extracted edited image filenames as input1 and input2? I hope someone can help. Thanks Emma