Hi Matt, It's this sequence: http://cni.stanford.edu/wiki/MR_Protocols#T2_weighted_scans (the 3D T2)
You can click the console screenshots for a closer view of the parameters -- let me know if you need me to track down more info. mw On Fri, Sep 27, 2013 at 11:38 AM, Matt Glasser <m...@ma-tea.com> wrote: > Someone sent me a different kind of T2w image and it didn't work so well, > so we need to know what kind of image this is. > > Peace, > > Matt. > > On 9/27/13 1:33 PM, "Bruce Fischl" <fis...@nmr.mgh.harvard.edu> wrote: > > >nope, pretty much only with T2-space with and without a flair pulse > >On Fri, > >27 Sep 2013, Matt Glasser wrote: > > > >> 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. > >> > >> > >> > >> > > >
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