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Hi, This error is because you have not given it an output name! That erroneous part is "… -out -omat 1.mat …" So it interprets "-omat" as the output name, and then thinks that 1.mat is now an option name, and hence declares it as an unrecognised option. Also note that you should only register images with anatomical features (not functional or blood flow maps). If the CBF images are derived from images with visible anatomical features then you should use those to do the registration and then apply that transformation to any maps derived from the analysis. If your "CBF" image actually has anatomical features (everywhere in the brain) then that's fine - I'm just warning you as I'm not quite sure what is in your "CBF" image. All the best, Mark On 24 Jan 2013, at 17:32, Maryam Abaei <[log in to unmask]> wrote: > Dear FSL experts, > > I am trying to register CBF map from ASL to MNI space using FLIRT however I am getting following error: > > > /usr/share/fsl/5.0/bin/flirt -in /home/mszma3/Maryam/013/035/208_007_3D_ASL_pre_exercise_20120611/lc_pc_035_0072-001_20120611_208_700_CBF_BET.nii.gz -ref /usr/share/fsl/5.0/data/standard/MNI152_T1_2mm_brain -out -omat 1.mat -bins 256 -cost corratio -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -dof 12 -interp trilinear > Unrecognised option 1 > Finished > > When I try using registration in melodic for the same data (giving 3D image instead of 4D), it works and register CBF to MNI. > > Now I would like to know how I can fix this error and use FLIRT. > > Thank you in advance. > Regards, > Maryam >