I'm sure it was registered to the T1w with BBR, though I don't know the internals of that in recon-all. Given that you might only be the second person to try this with non T2-SPACE T2w images (and I unfortunately had not told Bruce about my bad experience with this), you can forgive the FreeSurfer docs for not mentioning it yet. :)
That being said, it isn't guaranteed not to work, you just might have to do some fiddling with the nsigma parameters to get it to work, as the defaults for T2-SPACE are probably not good for your images. Peace, Matt. From: Michael Waskom <mwas...@stanford.edu> Date: Friday, September 27, 2013 10:06 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 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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