Hello,
I am interested in looking at ventricular changes over time and thus, have ran the longitudinal stream on my participants scans. As suggested online, I am checking the ventricular segmentation in the longitudinal outputs and am planning on making any edits to the longitudinal stream if the segmentation of the ventricles are incorrect. I have a few questions related to this:
1) To check the segmentations, should I overlay the aseg.mgz with the brainmask.mgz or the brainmask_SubjID-Temp.mgz?
2) If I find that the segmentation of the ventricle is incorrect, should I make edits to the aseg output in the longitudinal outputs? What command line would I use to re-do the longitudinal stream with the corrected segmentation?
3) After looking to see whether there are errors in the longitudinal recon-all script output, are there any other things I should check to ensure that the base and longitudinal stream ran correctly?
Thank you in advance for your help! Tamara