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Dear Doug,
Special appreciation for your help. Actually, I have created the annotation and the color table files and finally I have divided the parcels. Also, I checked the primary and the division parcels on the .pial surface that they were correct. But as I bring them from surface to volume using mri_aparc2aseg (as mentioned in the email, Subject: How to Create Cortex Parcellation Using "mri_aparc2aseg"?) it fail. I mean that the parcels are not placed where they should be there. In other word, I expect it when a primary region had been divided to for example two other regions finally, the two regions with each other form the primary region with the same shape and position in the brain cortex. But, it does not happen!!! All newly resulted regions are in the brain cortex and seem well in total but they do not placed correctly based on primary regions and have movement and region shape deformation when put them beside each other to have a one region as one of the primaries. So that I doubt about the freesurfer commands that basically are used for adults, while I use neonate images. I am really confused, I would appreciate it if you could help me.
Best Regards, Mahshid