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Hi, I'm not exactly sure what you are describing here. Do you find that part of the brain is in the image but is it cut-off at the edge of the image? If so then the problem is probably that the FOV of your highres image is larger than the one you've made with fslcreatehd. You should ideally use the same FOV (i.e. if the highres had 210mm in X, then 70 x 3 mm voxels is fine, but if it is 240mm then you need 80 voxels if each voxel is 3mm; in Z you currently only have 34 x 3.3 = 112.2 mm, so see if you need more voxels here). If this does not help then please email us and provide more information about what you are seeing. All the best, Mark On 18 Sep 2014, at 12:39, Francesca Strappini <[log in to unmask]<mailto:[log in to unmask]>> wrote: Hi Mark, Thanks for your reply, I have been really puzzled about this... I think it is something with the display range! I see some leftover brain in the top. how do I change it? Does this mean that if I load the files into matlab their data matrix will be aligned with the anatomy? I need to register several functional runs to the native anatomy and then load them into matlab and run correlations between them (they need to be aligned for that purpose). About the FOV, for some of my subjects I do see differences in "zoom" between the anatomy and the functional scans (the anatomy seems smaller). Best, [https://ssl.gstatic.com/ui/v1/icons/mail/images/cleardot.gif]Francesca 2014-09-17 20:02 GMT+02:00 Mark Jenkinson <[log in to unmask]<mailto:[log in to unmask]>>: Hi, The command looks OK (except for the last name being .nii.gz_tmp rather than _tmp.nii.gz, but I assume this is a typo in this email). Are you sure that the image contains zeros and not just that the display range is incorrect? Alternatively, the FOV of your new image might be too small in z. All the best, Mark On 15 Sep 2014, at 17:38, Francesca Strappini <[log in to unmask]<mailto:[log in to unmask]>> wrote: Dear Mark, Thank you for your suggestion. I have tried running it and when I open the output file in fslview, I see nothing (it uploads the file but there is no brain showing). The command I ran is as follows: /usr/local/fsl/bin/fslcreatehd 70 70 34 1 3 3 3.3 1 0 0 0 16 <name of output nii>_tmp.nii.gz ; /usr/local/fsl/bin/flirt -in <name of input nii> -applyxfm -init <Feat directory>/reg/example_func2highres.mat -out <name of output nii> -paddingsize 0.0 -interp trilinear -ref <name of output nii>.nii.gz_tmp Can you please tell me what is wrong with this command? or is there another way to view the output? Thank you very much for all your help.