Dear Developers,
I have a significant problem when rerunning the pial edits for the longitudinal data. Our dataset consists of subjects & a followup scan (for each sub). To be thorough, we edited brain.finalsurfs.manedit.mgz (as it was further in the processing stream) for the cross-sectional scans, the base scans, and the longitudinal scans. The longitudinal data were created only after the base has been edited and rerun. Likewise, the base was only created and rerun after the cross-sectionals were finalized.
We work with a clinical population so minor edits do show up on the longitudinal scans. However, after editing and recreating the surfaces from these longitudinal scans, the pial surfaces has extended to include dura & other voxels that were not previously included within the pial surface (during the initial creation of the longitudinal data). We tried both commands (listed below) and get this same problem:
recon-all -autorecon2-pial -autorecon3 -long tpN tp_base ( http://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalEdits) or recon-all -autorecon3-pial -long tpN tp_base ( http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/LongitudinalTutorial)
*Could you please help us figure out why the pial surface extends to include nonbrain regions when recreating the surfaces? * * * *What solutions would you suggest in resolving this problem?* * * Thank you,
Vy Dinh Research Associate Department of Neurological Sciences Rush University Medical Center