Hi everyone,
I recently tried to run a paired T-test in SPM on a repeated measures dataset with fMRI data. When I looked at the contrasts, it showed activation in regions outside the brain, which suggested to me that there was a masking issue. I tried to mask the images using fslmaths -mas, but when I re-ran the analysis, I got the exact same results, which suggested I didn’t properly mask the data. I want to mask the functional data to an MNI brain.
I ran this command with fsl: fslmaths ‘path to original functional image’ -mas ‘path to MNI brain’ ‘name for new masked file’
When I did so, it created a a file called -mas.nii, which is not the name I wanted for this file.
Any help would be appreciated!