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 mwaskom@stanford.edu Date: Friday, September 27, 2013 2:20 PM To: Matt Glasser matt@ma-tea.com Cc: Bruce Fischl fischl@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 matt@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" fischl@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" fischl@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 >>>mwaskom@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.