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Dear Joyce, Sorry I forgot to tar all images, which I did so just now. The name of the tar file is DTIFIT_Joyce.tar. I have used DTIFIT GUI, command line was /usr/share/fsl/5.0/bin/dtifit --data=/home/guo/DTI/1.5T/00/test/eddy_dti_c003.nii.gz --out=/home/guo/DTI/1.5T/00/test/dti --mask=/home/guo/DTI/1.5T/00/test/c003_SPGR_brain.nii.gz --bvecs=/home/guo/DTI/1.5T/00/test/dat_001.nii.gz.bvecs --bvals=/home/guo/DTI/1.5T/00/test/dat_001.nii.gz.bvals, which was created after 'GO' botton on DTIFIT GUI was pressed. Thanks! the problem is that you have been using a brain mask in the space of (with the dimensions of) the structural scan. Your output will then also be in that space, and in that space your diffusion data will end up in one of the corners (outside the mask). It appears that dtifit doesn’t check to see that the dimensions of the diffusion data and the mask is the same. Maybe that is something we should consider for the future. For you, the best solution is to base the mask on the b0 of your diffusion data. I did fslroi eddy_dti_c003.nii.gz b0 0 1 bet b0 brain -f 0.3 -m dtifit -k eddy_dti_c003.nii.gz -o rubbestad -m brain_mask.nii.gz -r dat_001.nii.gz.bvecs -b dat_001.nii.gz.bvals and that worked well. Jesper