Just to clarify a bit. When I ran the independent FLIRT CLI, I output a 4D.nii.gz file and a mat file. The names of those files are specific to my data, i.e., are labeled "sub1-cond1-4D.nii.gz" and "sub1-cond1-4D.mat". Should I rename them with "example_func2standard" when I replace the files created in the reg directory during the first level analysis? In other words, is the naming convention important for files in the reg directory? Thanks again.
Catherine
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