I believe the following link from my FAQ should help you understand things better: http://research.baycrest.org/~jimmy/UseANALYZE.htm I have two notes regarding to FSL (5 & 6). Note 6 said: The display of FSL doesn’t seem like the orientation in the table; however, if you pay attention to the flipped R / L labels beside the Axial / Coronal views, you will find that the orientation is actually also flipped. Now, let's take a look how FSL View is different from other NIfTI applications (e.g. my NIfTI tools): 1. Take a T1 image. If you don't have, you can take either "avg152T1_LR_nifti.nii" or "avg152T1_RL_nifti.nii" from NIfTI web site, which is modified from standard T1 image. You may notice that standard T1 image is in Analyze 7.5 format, and avg152T1_LR_nifti / avg152T1_RL_nifti are in NIfTI format. This doesn't matter, because in following step, we will make a NIfTI image based on T1. 2. Use my "load_nii" to load the image, and use my "view_nii" to view the image. Change voxel location to [21 54 35]. Click "Edit" menu, and choose "Edit voxel value at crosshair". Input 0 in the edit box, and click "OK". Click "File" menu, and choose "Save displayed image as". Let's call it "N215435.nii". This is a NIfTI image. At left hemisphere, there is a black dot. The location is [21 54 35] in voxel, and [-50 -20 -4] in millimeter. 3. Launch "FSL View". Click "File" menu, and open "N215435.nii". You will find that the black dot is now at right hand side, and is exactly at location [-50 -20 -4] in millimeter. However, if you pay attention to FSL label, you can find that the big "L" (left) is at RHS. Therefore, there is no laterality issue here, but just some confusion, which is described in my note 6 above. 4. You may also notice that the location in FSL View is [20 53 34] in voxel, rather than [21 54 35] in voxel. This is because in FSL View, the 1st voxel is [0 0 0] instead of [1 1 1]. Click the minus sign at RHS of voxel location in FSL View window, and you can find that. Conclusions: The numbers of mm are NOT different. There is NO left-rigth reverse. You don't need to do anything to correct it. However, You need to thoroughly understand this, and DO NOT pick the wrong voxel in FSL View window. [48 -18 -2] is NOT the voxel in [21 54 35] / [-50 -20 -4]. [20 53 34] is the right one.