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Dear Mark I have been trying different options about fnirt command problem in order to solve it, but for some reason I have not find where is the error: 1. fnirt --in=T1.nii.gz --aff=T1_to_MNI.mat --cout=T1_to_MNI_warp.nii.gz --config=T1_to_MNI152_2mm *Cannot find config-file T1_to_MNI152_2mm* rosi@rosi-HP-Pavilion-dv9700-Notebook-PC:~/Desktop/aag_c$ 2. rosi@rosi-HP-Pavilion-dv9700-Notebook-PC:~$ cd /home/rosi/Desktop/aag_c rosi@rosi-HP-Pavilion-dv9700-Notebook-PC:~/Desktop/aag_c$ fnirt --in=T1.nii.gz --aff=T1_to_MNI.mat --cout=T1_to_MNI_warp.nii.gz --config=T1_to_MNI152_2mm.cnf *Cannot find config-file T1_to_MNI152_2mm.cnf* 3. rosi@rosi-HP-Pavilion-dv9700-Notebook-PC:~/Desktop/aag_c$ fnirt --in=T1.nii.gz --aff=T1_to_MNI.mat --cout=T1_to_MNI_warp.nii.gz --config=/usr/share/fsl/data/standard/T1_to_MNI152_2mm.nii.gz *Cannot find config-file /usr/share/fsl/data/standard/T1_to_MNI152_2mm.nii.gz* Any one could tell me where is the problem? I have been reading about configuration files in the fsl web, but I were not able to find the solution. Best regards, Rosalia.