I was using FSL for the last 4 years on centOS. If I apply a motion correction for example it puts the motion corrected image in the same folder as the source. Now I loaded UBUNTU and it creates a new folder under the source folder and puts it there. And it does this for all the FSL tools (such as fslmaths, flirt...) by creating a new folder, so all my previously written scripts needed to be modified. I would like to ask you, is there a change that I could apply in somewhere, by the way I could get all the new calculated images in the same folder?