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Russ one potential "cheat" that I think would work is to use fslmaths to add a L or an R to your original image (just draw one in FSLVIEW) and just follow it through the processing pipeline. I don't know why programs just don't let you pick a blank area within your FOV but not within the brain to allow this sort of thing easily, but it should be pretty easy if you play aroudn with fslmaths input_image -add LEFT_MARKER input_image_with_marker DG. On Fri, Apr 4, 2008 at 10:29 AM, Russell Poldrack <[log in to unmask]> wrote: > 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 > -- David A Gutman, M.D. Ph.D. Department of Psychiatry & Behavioral Sciences Emory University School of Medicine