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Hi, This is another bug (I think) with FSLView where files with no data in them (all zeros) crash it on load. Alternatively, some FSL programs may create a bad file when they produce a result with only zeros. I am guessing that your highres mask is only a single slice thick, and thus is being interpolated to a lower value than .5. Try loading the transformed mask (before binarization) to get a feel for what value you should set the threshold to. Peace, Matt. -----Original Message----- From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf Of David Roalf Sent: Wednesday, August 22, 2007 2:02 PM To: [log in to unmask] Subject: Re: [FSL] Coverting Standard Mask back to native space Thanks for all your help so far! I think we're almost there... We have completed the steps to transform our masks into native space very thoroughly and with much success, up until the thresholding step. We can open and view our data after creating the 'highres_mask.' The next command: 'avwmaths highres_mask -thr 0.5 -bin highres_mask' appears to alter our data in some way but when attempting to open and observe the images with FSL View it causes the program to crash each time. This step causes us to be incapable of viewing the new mask file. Is there an obvious issue with our command line that needs to be altered? Should the last two steps in the transformation be completed as a single command and not two separate commands? Thank you! D. Roalf