The differences have been found in the outputs from the aseg file. Particularly, I am interested in the ventricles and the intracranial volumes. I have loaded both anatomicals in FreeView and toggled between them and have found no differences visually.
I have attached the files (Via Google Drive since they are large). They are from the same participant.
Thank you again, Tamara
rawavg_MriConvert.mgz https://drive.google.com/file/d/0B2XDrkcQhdARTFdYZHpwR2doTXc/view?usp=drive_web rawavgSlicer4.mgz https://drive.google.com/file/d/0B2XDrkcQhdARV1dtZW1PZ1Z1ODA/view?usp=drive_web