Was wondering if anyone from the Freesurfer team is looking into this issue yet.
On Fri, Mar 29, 2013 at 10:13 AM, Vy Dinh <vy_d...@rush.edu> wrote: > 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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