Also, what kind of T2w sequence is this? I think we've mostly tested it with the T2-SPACE (unless Bruce has tested with other things).
Peace, Matt. On 9/27/13 12:58 PM, "Bruce Fischl" <fis...@nmr.mgh.harvard.edu> wrote: >Hi Michael > >that looks pretty bad! What is the resolution of the T2? The T1 that you >overlay on also looks somewhat blurry - what was it? > >Bruce > > >On Fri, 27 Sep >2013, Michael Waskom wrote: > >> 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 >> >> >> >>_______________________________________________ >Freesurfer mailing list >Freesurfer@nmr.mgh.harvard.edu >https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > >The information in this e-mail is intended only for the person to whom it >is >addressed. If you believe this e-mail was sent to you in error and the >e-mail >contains patient information, please contact the Partners Compliance >HelpLine at >http://www.partners.org/complianceline . If the e-mail was sent to you in >error >but does not contain patient information, please contact the sender and >properly >dispose of the e-mail. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
