BTW, we are using Freesurfer 5.1: freesurfer-i686-apple-darwin9.8.0-stable5-20110525
On Fri, Mar 29, 2013 at 10:08 AM, Vy Dinh <vy_d...@rush.edu> wrote: > 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 >
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