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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