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Hi - In this case it would be best to resample the fdt_paths back to native space before calculating your mean FA values. Cheers Saad On 3 Nov 2016, at 13:59, Noelia Martinez Molina <[log in to unmask]<mailto:[log in to unmask]>> wrote: Dear FSL experts, I've run probtrackX and my fdt_paths are in MNI space. In order to extract the mean FA value from this "probability of connection" thresholded at 0.01, I used the following command: fslstats fadiffimage.nii.gz -k fdt_paths.nii.gz -M However, my fadiffimage is in native space so I got the error: "Mask and image must be the same size". Before I go forward, I'd like to confirm whether the correct solution to this would be to transform the fadiffimage to MNI space using flirt. (Please my apologies if this has already in discussed in a previous thread, I couldn't find it). Thank you in advance for your help, Noelia