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 matt@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 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
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