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Hi,
I'm new to this and was wondering if someone could help me out? I used a T1 preprocessed image (fmriprep), normalized to the NIH pediatric cohort 6 (13-18.5 years) template to do recon-all and then used the hippocampal segmentation tool v.7. I have two questions: a) wouldn't one expect the segmentation to be the same for different individuals if the normalized T1's are used (registration seems to be well aligned to the same space when checked in SPM but when looking into the .txt files the volumes are different)? and b) (how) do I need to use the -custom-tal-atlas flag to get the estimates back to the NIH pediatric atlas (cohort 6) and can I make masks from the hippocampal segmentations for ROI analysis in other software for this study population?
Thank you!