cheers,

satra

On Tue, Nov 20, 2012 at 7:53 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote:

yes, that's probably true. The FLAIR we use is just a T2-SPACE scan with an inversion pulse to put CSF at the null point, so if you can get T2-space at .7 you should be able to get FLAIR (although you do burn some SNR with the inversion)

On Tue, 20 Nov 2012, Matt Glasser wrote:

Hi Bruce,

Can you get good FLAIRs at 0.7mm isotropic?

The fluid thing makes sense for surface reconstruction, but I think it
would mess up myelin maps if someone also wanted to do that using the
ratio method. If the CSF is now dark and you divide the dark CSF in the
T1w with dark CSF in the T2w, you would get unpredictable results in the
partial volume region along the edge.

Thanks,

Matt.

On 11/20/12 6:27 PM, "Bruce Fischl" <fischl@nmr.mgh.harvard.edu> wrote:

Hi Satra

the T1 maps accomplish much of what the ratio does - it gets rid of
receive bias effects. I'm not really sure which is better. They are about
the same amount of scan time.

The advantage of including the flair inversion pulse in the T2 space is
that it nulls fluid and lets intensities by monotonically decreasing
moving
outwards from the gray/white boundary. This makes partial volume effects
less of a problem. Dura is also pretty much totally absent from the FLAIR
and in the prelim data that we've processed having the FLAIR images lets
the surface recover from pretty much all mistakes in which dura is
included
in the pial surface.

cheers
Bruce

On Tue, 20 Nov 2012, Matt Glasser wrote:

If you make a T1 map you can use that to look at differences in myelin
content, but I don't know all of the ways to calculate T1 or if you
could
get that from only two flip angles. Two images with roughly the same
contrast won't work for the ratio method. You need to have opposite
contrast.

Also I'm not sure how a FLAIR would be better than a T2-SPACE.

Peace,

Matt.

From: Satrajit Ghosh <satra@mit.edu>
Date: Tuesday, November 20, 2012 5:51 PM
To: Matt Glasser <matt@ma-tea.com>
Cc: "Watson, Christopher" <Christopher.Watson@childrens.harvard.edu>,
"Winter, Warren" <Warren.Winter@childrens.harvard.edu>,
"freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Tool for incorporating T2-SPACE data in pial
surface recons?

hi
matt: could you generate the myelin maps say from two flash scans at
different flip angles?
bruce: if one had a choice between an mprage + t2 flair and 2 flash
scans at
5/20 flip angles, what would be your recommendation?

cheers,

satra

On Tue, Nov 20, 2012 at 6:35 PM, Matt Glasser <matt@ma-tea.com> wrote:
If you get an MPRAGE and T2-SPACE you can make myelin maps too.
FreeSurfer's final surface placement benefits a lot from high
resolution
images (less than 1mm) and you can still get good SNR with when
you use
32-channel coils.

Peace,

Matt.

On 11/20/12 4:41 PM, "Bruce Fischl" <fischl@nmr.mgh.harvard.edu>
wrote:

>Yes, definitely. The t2-space flair is a big help
>
>
>
>On Nov 20, 2012, at 5:40 PM, "Watson, Christopher"
><Christopher.Watson@childrens.harvard.edu> wrote:
>
>> Hi Bruce,
>> So would you recommend acquiring a T2 in addition to an
>>(ME)MPRAGE/SPGR? i.e. is it worth squeezing another
acquisition into a
>>protocol?
>>
>> Chris
>> ________________________________________
>> From: freesurfer-bounces@nmr.mgh.harvard.edu
>>[freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce
Fischl
>>[fischl@nmr.mgh.harvard.edu]
>> Sent: Tuesday, November 20, 2012 3:01 PM
>> To: Winter, Warren
>> Cc: freesurfer@nmr.mgh.harvard.edu
>> Subject: Re: [Freesurfer] Tool for incorporating T2-SPACE
data in pial
>>surface recons?
>>
>> Hi Warren
>>
>> yes, it will be part of the upcoming 5.2 release, hopefully
in Dec. It
>> will use either a FLAIR or T2 (ideally T2-SPACE for either
one)
>>
>> cheers
>> Bruce
>> On Tue, 20
>> Nov 2012, Winter, Warren wrote:
>>
>>> Hi all,
>>>
>>> Back in January and October Bruce mentioned that he had
under
>>>development some scripts designed to utilize T2-SPACE images
for better
>>>pial surface reconstruction in the presence of dura -- I was
just
>>>wondering if any of that is ready for trial?
>>>
>>> Thanks!
>>>
>>> Warren
>>>
>>> --
>>> Warren Winter
>>> Research Coordinator
>>> Boston Children's Hospital
>>> Sheridan Laboratory of Cognitive Neuroscience
>>> Division of Developmental Medicine
>>> 1 Autumn Street, AU 650
>>> Boston, MA 02215
>>> 857-218-5224
>>>
>>>
>>> _______________________________________________
>>> Freesurfer mailing list
>>> Freesurfer@nmr.mgh.harvard.edu
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>
>>>
>>>
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