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Is it possible that you have spaces in the file names and/or directory? What's the exact command you are running for the cases that are causing problems? What is the output of pwd ? On Thu, Feb 12, 2015 at 5:28 PM, SUBSCRIBE FSL Claire Burns < [log in to unmask]> wrote: > Hi, > > We've been using the fsl_motion_outliers tool with the DVARS metric, but > for two of our fMRI scans it won't create a motion file. We've been running > the command: > > fsl_motion_outliers -i <subject>.nii.gz -o <subject>_motion --dvars > > It has worked for almost all of our subjects, but for two of the scans it > will run but the motion file won't save to the folder. We've tried saving > it to other folders as well in case that's the issue but it still doesn't > show up. We're not sure why this is only happening for a couple scans since > we're running everything the same way, and aren't getting any error > messages. > > Thanks, > Claire > -- Niels Bergsland Integration Director Buffalo Neuroimaging Analysis Center 100 High St. Buffalo NY 14203 [log in to unmask]