Hi, just to make the problem a bit more transparent, I took a second screenshot of the slices with the pial surface from the -T2pial run in red and the pial surface from the normal run in cyan: https://dl.dropbox.com/s/jv8rcxnq50tdac6/bad_slice_both_pial.png
On Fri, Sep 27, 2013 at 10:37 AM, Michael Waskom <mwas...@stanford.edu>wrote: > Hi, > > I'm using FS 5.3 and trying to use hires T2-weighted scans to refine the > pial mesh. > > However, I've found that using the T2 is causing rather dramatic problems > with the pial surface. > > I processed the same subject's data with and without the -T2pial option. > Here are links to a) pial surface image b) slices through the volume and c) > the recon-all.log: > > With -T2pial > ---------------- > https://dl.dropbox.com/s/rtjgplajfptr4xb/bad_surf_withT2.png > https://dl.dropbox.com/s/d7so5qtujgg8j80/bad_slice_withT2.png > https://dl.dropbox.com/s/7o00jy014hihrgu/recon_log_withT2.txt > > Without -T2pial > -------------------- > https://dl.dropbox.com/s/51y15kogecltfbi/bad_surf_noT2.png > https://dl.dropbox.com/s/3gps45kp0ngkuli/bad_slice_noT2.png > https://dl.dropbox.com/s/6jih6f8fh4nwh0k/recon_log_noT2.txt > > The release notes for 5.3 claim that the T2 is registered to the T1 before > refining the surface, but I actually can't find any evidence of that > sequence in the log file. For this subject, the T1 and T2 came from > different scan sessions, although I have other data where they were > acquired in the same session that have similar, if less dramatic, problems > with the pial surface. > > Any ideas? > > Michael >
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