hmmm. That would be strange and would result in complete failure (which I
guess is what you have seen). For what it's worth, Matt is right and we
haven't tested the code on many datasets, but at least so far it has been
independent of contrast (that is, it works on both T2 and FLAIR)
cheers
Bruce
On Fri, 27
Sep 2013, Michael Waskom wrote:
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
>>>>
>>>>
>>>>
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