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Most of the FSL tools ignore the NIfTI spatial transforms (both QForm and SForm). Additionally, the templates included with FSL tend to be left-right reversed from orthogonal space (ie, the template matrix is -2 0 0; 0 2 0; 0 0 2 instead of 2 0 0; 0 2 0; 0 0 2). Therefore, you need to be very careful when using FSL for normalization. I would ensure the images are not flipped during the non-linear registration. >>> Morten Bruvold <[log in to unmask]> 08/19/11 9:54 AM >>> Hi, I receive this error message when trying to run randomise on tbss_sym data from the tool "Testing left vs. right in TBSS": randomise -i all_FA_skeletonised_left_minus_reight.nii.gz -o randomiseLRdiff -1 -v 5 -T ERROR: Program failed An exception has been thrown Data mask is blank. Exiting I tried first dcm2nii and then MRIconvert for conversion of data to nifti. Both give the same error. When viewing the mean_FA_skeleton_mask i can see the proper mask image. Do anyone have a clue about what could be wrong? Regards, Morten The information in this transmission is intended for official use of the Kessler Foundation. It is intended for the exclusive use of the persons or entities to which it is addressed. If you are not an intended recipient or the employee or agent responsible for delivering this transmission to an intended recipient, be aware that any disclosure, dissemination, distribution or copying of this communication, or the use of its contents, is strictly prohibited. If you received this transmission in error, please notify the sender by return e-mail and delete the material from any computer.