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Sorry to clutter your mailboxes with more questions about nifti, but I am trying to make sure that I am correctly understanding things. We have a preprocessing script that was originally developed to work with Analyze images, but some of our users have since used it with Nifti as their output type. I am certain that the resulting orientation is correct, but I want to make sure that I completely understand what is happening when people go from analyze to nifti. Here is the stream: 1. Convert from DICOM to Analyze 3D using the LONI Debabeler - this creates images stored in radiological convention, but they do not have the customary negative X dimension value for FSL. 2. create 4D file - when this was done using fsl 3 with analyze as the output type, the files would automatically have the x dimension set to negative, and thus header and data were in sync - however, when output type is set to nifti, the resulting nifti images have a positive sform and are classified by fslorient as neurological; header and data are thus out of sync 3. do preprocessing and first-level analysis - throughout these steps, the derivative nifti images retain the neurological format 4. create registered images at 2nd level - at this point, the resulting registered images now have a header that specifies radiological storage. it would appear that data and header are back in sync, assuming that no flipping occurred during registration. What I need to confirm is that the second-level analysis is NOT flipping the actual data in the move from neurological to radiological convention. I am pretty certain that this is the case (since the motor cortex activation shows up on the correct side in the registered maps) but I want to make absolutely sure that there is not something else happening that I am missing. thanks! russ --- Russell A. Poldrack, Ph.d. Associate Professor Wendell Jeffrey and Bernice Wenzel Term Chair in Behavioral Neuroscience UCLA Department of Psychology Franz Hall, Box 951563 Los Angeles, CA 90095-1563 phone: 310-794-1224 fax: 310-206-5895 email: [log in to unmask] web: www.poldracklab.org