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> > I have some questions about fMRI normalization in Spm99. > > > > Our fMRI scans after normalization looks bigger and the shape seems > > distorted(attached a pictures). The steps we did are: 1. Realign with > > option coregist with reslice. 2. Normalize with EPI.img from spm99 > > template We then used the normalization parameter set > > "means5-009.sn3d.mat" generate by preprocessing of fMRI scans, to write > > our normalize anatomical T1 scan. The results also seem to be much > > bigger than canonical/single_subj_T1.img, and part of the brain is > > cut off. (please see attached picture ) We compare the results by > > overlay ing our fMRI activation map on canonical/single_subj_T1.img on > > our normalized structures img, all active region are shift up a lot on > > our coregistered activation map and structural images (please see > > attached pictures). > > > > The original fmri scan has 16 slices, vox size is 3.75 * 3.75 * 9mm. Our > > fmri img & anatomical img after normalization the dimension is 79 95 68 > > origin is 39 38 42. But the template EPI.img & canonical/avg152.img 's > > dimensions is 91 109 91, origin is 46 64 37. Is that maybe the reason our > > normalization is not correct? Thank you for your suggestions . My first suggestion about how to improve the spatial normalisation would be to brain-masking via the defaults button. This is not needed for spatial normalisation based on fMRI, and should make the procedure much more stable. Best regards, -John -- Dr John Ashburner. Functional Imaging Lab., 12 Queen Square, London WC1N 3BG, UK. tel: +44 (0)20 78337491 or +44 (0)20 78373611 x4381 fax: +44 (0)20 78131420 http://www.fil.ion.ucl.ac.uk/~john