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Dear Martha, I've just found that you have selected the "No Search" option on the highres to standard space registrations in the multiple subject case and "Normal Search" in the single subject case. I'm not sure if there are more differences as well (for instance in the Featquery calls) but this difference at least explains the small differences you are seeing in your registrations. All the best, Mark On 9 Dec 2011, at 17:43, Martha Shiell wrote: > Thank you Mark, > > The reference number is 915957. > I have separated the files into two folders, one (multiple_subjects) from when the single design included multiple inputs (the subject of interest is the first input), and the other from when the design was for a single subject (single_subject). > > I am sure that I have used the same images for both runs and the DOF for the registration are the same. > > I also included the mask.nii.gz and the report.log files from the featquery that I ran on the two Feat directories. The difference in the mask.nii.gz images is what alerted me to the difference in /reg files. However, maybe there is another explanation for the difference in mask.nii.gz files? > > I really appreciate your input, thank you again, and please let me know what other information you might require. > > Martha >