Hi!
For my manuscript, the journal wants me to answer some questions on the methods that I used and I want to make sure I am giving correct information on how FreeSurfer calculates hippocampal volumes. Would it be possible to check my 4 answers and let me know if these are accurate?
Question: How were the data normalized/standardizes? Answer: T1 data was intensity normalized using FreeSurfer's mri_normalize script
Question: Describe the template used for normalization/transformation Answer: All data was kept in subject-specific space, no templates were used. FreeSurfer, volumes are defined in several steps during which a high-dimensional non-linear registration is done to the MNI305 template to increase the accuracy of the segmentation and to facilitate the segmentation and tissue-probability assessment for region labeling. Volumes of the hippocampus are ultimately extracted from a subject-specific subcortical volumetric atlas (aseg) in 1mm isotropic space.
Question: Describe your procedure for artifact and structured noise removal Answer: The standard preprocessing pipeline of FreeSurfer incorporates motion correction, intensity correction and skull-stripping.
Question: how are anatomical locations determined? Answer: In FreeSurfer a subject-independent probabilistic atlas (hand labeled atlas by neuroanatomists on a training set) and subject-specific measured values. Subject-specific segmentations of the hippocampus are based on these probabilities and on the white and pial surfaces.
Many thanks! All the best Heidi