Hmm, Ok. Thanks Matt. I still think it's weird that the T2 didn't seem to ever get registered to the FS volume, but it's not a huge loss if we can't use them. With that said, it might help to clarify the docs on this point a bit, as it sort of sounded like any reasonably-sized T2-weighted image would be useful, and I would have tried to collect a different image if I had known!
On Fri, Sep 27, 2013 at 12:58 PM, Matt Glasser <m...@ma-tea.com> wrote: > So the T2-SPACE is a variable flip angle sequence that actually has a fair > amount of T1 and MT contrast in it and relatively less T2 contrast. As a > result, you can clearly see the difference between grey and white matter, > and CSF is not massively brighter than grey and white matter. If you are > using a different kind of T2w sequence where the distance between CSF > intensity and grey matter intensity is much greater, some of the internal > settings to the -T2pial flag will likely not be optimal. I don't know if > recon-all allows you to modify those with expert options or not. Bruce, is > it possible for the user to modify the –nsigma_above and -nsigma_below > flags for mris_make_surfaces when using -T2pial? > > Peace, > > Matt. > > From: Michael Waskom <mwas...@stanford.edu> > Date: Friday, September 27, 2013 2:20 PM > To: Matt Glasser <m...@ma-tea.com> > Cc: Bruce Fischl <fis...@nmr.mgh.harvard.edu>, " > Freesurfer@nmr.mgh.harvard.edu" <Freesurfer@nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] Major problems with T2-based pial removal > > 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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