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Hi, I am trying to coregister a 3-slice EPI to a low-resolution anatomical (t2 flair) image. The anatomical image covers the whole brain and has the 3 EPI slices as a subset. Slice thickness is 6 mm in both cases. Thus, I need a flirt command with Z translation only: Case 1: flirt -in epi_3 -ref T2flair_brain -out epi_3_in_T2flair -schedule /usr/local/fsl/etc/flirtsch/ztransonly.sch Result: The coregistration (location of slices) is ok but there are only 2 EPI slices in the anatomical space Case 2 (-2D): flirt -in epi_3 -ref T2flair_brain -out epi_3_in_T2flair -2D -schedule /usr/local/fsl/etc/flirtsch/ztransonly.sch Result: Now there are 4 EPI slices. What is going on here? Cheers, Teemu Rinne Dept Psychology Univ Helsinki, Finland Flirt versio is 5.4.2 (mac g5 & intel mac pro). avwinfo T2flair_brain: dim1 512 dim2 512 dim3 28 dim4 1 datatype 4 pixdim1 0.4296880066 pixdim2 0.4296819866 pixdim3 6.0000000000 pixdim4 1.0000000000 cal_max 302.0000 cal_min 0.0000 glmax 0 glmin 0 origin1 257 origin2 1 origin3 256 file_type ANALYZE-7.5 avwinfo epi_3: data_type dim1 128 dim2 128 dim3 3 dim4 1 datatype 4 pixdim1 -1.7187500000 pixdim2 1.7187299728 pixdim3 6.0000000000 pixdim4 1.0000000000 cal_max 3034.0000 cal_min 0.0000 glmax 0 glmin 0 origin1 16640 origin2 16384 origin3 256 file_type ANALYZE-7.5