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
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