[Freesurfer] Tool for incorporating T2-SPACE data in pial surface recons?
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 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.
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 > > > ___ 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.
Re: [Freesurfer] Tool for incorporating T2-SPACE data in pial surface recons?
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-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fis...@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 > > > ___ 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. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Tool for incorporating T2-SPACE data in pial surface recons?
Yes, definitely. The t2-space flair is a big help On Nov 20, 2012, at 5:40 PM, "Watson, Christopher" 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-boun...@nmr.mgh.harvard.edu > [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl > [fis...@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 >> >> >> > ___ > 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. > > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Tool for incorporating T2-SPACE data in pial surface recons?
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" wrote: >Yes, definitely. The t2-space flair is a big help > > > >On Nov 20, 2012, at 5:40 PM, "Watson, Christopher" > 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-boun...@nmr.mgh.harvard.edu >>[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl >>[fis...@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 >>> >>> >>> >> ___ >> 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. >> >> >> > >___ >Freesurfer mailing list >Freesurfer@nmr.mgh.harvard.edu >https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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 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" wrote: > > >Yes, definitely. The t2-space flair is a big help > > > > > > > >On Nov 20, 2012, at 5:40 PM, "Watson, Christopher" > > 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-boun...@nmr.mgh.harvard.edu > >>[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl > >>[fis...@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 > >>> > >>> > >>> > >> ___ > >> 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. > >> > >> > >> > > > >___ > >Freesurfer mailing list > >Freesurfer@nmr.mgh.harvard.edu > >https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > ___ 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.
Re: [Freesurfer] Tool for incorporating T2-SPACE data in pial surface recons?
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 Date: Tuesday, November 20, 2012 5:51 PM To: Matt Glasser Cc: "Watson, Christopher" , "Winter, Warren" , "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 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" wrote: > >> >Yes, definitely. The t2-space flair is a big help >> > >> > >> > >> >On Nov 20, 2012, at 5:40 PM, "Watson, Christopher" >> > 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-boun...@nmr.mgh.harvard.edu >>> >>[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl >>> >>[fis...@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 >>>> >>> >>>> >>> >>>> >>> >>> >> ___ >>> >> 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. >>> >> >>> >> >>> >> >> > >> >___ >> >Freesurfer mailing list >> >Freesurfer@nmr.mgh.harvard.edu >> >https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ 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.
Re: [Freesurfer] Tool for incorporating T2-SPACE data in pial surface recons?
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
Date: Tuesday, November 20, 2012 5:51 PM
To: Matt Glasser
Cc: "Watson, Christopher" ,
"Winter, Warren" ,
"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 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"
wrote:
>Yes, definitely. The t2-space flair is a big help
>
>
>
>On Nov 20, 2012, at 5:40 PM, "Watson, Christopher"
> 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-boun...@nmr.mgh.harvard.edu
>>[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce
Fischl
>>[fis...@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
>>>
>>>
>>>
>> ___
>> 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 yo
Re: [Freesurfer] Tool for incorporating T2-SPACE data in pial surface recons?
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" 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 >> Date: Tuesday, November 20, 2012 5:51 PM >> To: Matt Glasser >> Cc: "Watson, Christopher" , >> "Winter, Warren" , >> "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 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" >> wrote: >> >> >Yes, definitely. The t2-space flair is a big help >> > >> > >> > >> >On Nov 20, 2012, at 5:40 PM, "Watson, Christopher" >> > 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-boun...@nmr.mgh.harvard.edu >> >>[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce >> Fischl >> >>[fis...@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 >> &
Re: [Freesurfer] Tool for incorporating T2-SPACE data in pial surface recons?
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" 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 >>> Date: Tuesday, November 20, 2012 5:51 PM >>> To: Matt Glasser >>> Cc: "Watson, Christopher" , >>> "Winter, Warren" , >>> "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 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" >>> wrote: >>> >>> >Yes, definitely. The t2-space flair is a big help >>> > >>> > >>> > >>> >On Nov 20, 2012, at 5:40 PM, "Watson, Christopher" >>> > 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-boun...@nmr.mgh.harvard.edu >>> >>[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce >>> Fischl >>> >>[fis...@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 W
Re: [Freesurfer] Tool for incorporating T2-SPACE data in pial surface recons?
thanks matt and bruce. this is very helpful. cheers, satra On Tue, Nov 20, 2012 at 7:53 PM, Bruce Fischl 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" 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 >>>> Date: Tuesday, November 20, 2012 5:51 PM >>>> To: Matt Glasser >>>> Cc: "Watson, Christopher" >>>> >>>> >, >>>> "Winter, Warren" >>>> >>>> >, >>>> "freesur...@nmr.mgh.harvard.**edu " < >>>> freesur...@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 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" >>>> wrote: >>>> >>>> >Yes, definitely. The t2-space flair is a big help >>>> > >>>> > >>>> > >>>> >On Nov 20, 2012, at 5:40 PM, "Watson, Christopher" >>>> >>>> >> >>>> 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? >>>> >> >>>&g
Re: [Freesurfer] Tool for incorporating T2-SPACE data in pial surface recons?
sure. Note that whichever you do it's absolutely critical to bandwidth
and readout match them so there is no differential distortion between the
contrast types
Bruce
On Tue, 20 Nov 2012, Satrajit Ghosh wrote:
thanks matt and bruce. this is very helpful.
cheers,
satra
On Tue, Nov 20, 2012 at 7:53 PM, Bruce Fischl
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"
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
Date: Tuesday, November 20,
2012 5:51 PM
To: Matt Glasser
Cc: "Watson, Christopher"
,
"Winter, Warren"
,
"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
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
Re: [Freesurfer] Tool for incorporating T2-SPACE data in pial surface recons?
You can correct the readout distortion with a field map. The main residual is just signal loss in the gradient echo image. Peace, Matt. On 11/20/12 7:22 PM, "Bruce Fischl" wrote: >sure. Note that whichever you do it's absolutely critical to bandwidth >and readout match them so there is no differential distortion between the >contrast types >Bruce >On Tue, 20 Nov 2012, Satrajit Ghosh wrote: > >> thanks matt and bruce. this is very helpful. >> cheers, >> >> satra >> >> On Tue, Nov 20, 2012 at 7:53 PM, Bruce Fischl >> >> 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" >> 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 >> >> Date: Tuesday, November 20, >> 2012 5:51 PM >> To: Matt Glasser >> >> Cc: "Watson, Christopher" >> , >> "Winter, Warren" >> , >> "freesurfer@nmr.mgh.harvard.edu" >> >> Subject: Re: [Freesurfer] >> Tool for incorporating >>
Re: [Freesurfer] Tool for incorporating T2-SPACE data in pial surface recons?
Hi Matt I doubt you could accurately correct the 0.25mm distortions that would be widespread, not to mention the extra interpolation. Much better to distortion match the acquisitions Bruce On Nov 20, 2012, at 8:45 PM, Matt Glasser wrote: > You can correct the readout distortion with a field map. The main > residual is just signal loss in the gradient echo image. > > Peace, > > Matt. > > On 11/20/12 7:22 PM, "Bruce Fischl" wrote: > >> sure. Note that whichever you do it's absolutely critical to bandwidth >> and readout match them so there is no differential distortion between the >> contrast types >> Bruce >> On Tue, 20 Nov 2012, Satrajit Ghosh wrote: >> >>> thanks matt and bruce. this is very helpful. >>> cheers, >>> >>> satra >>> >>> On Tue, Nov 20, 2012 at 7:53 PM, Bruce Fischl >>> >>> 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" >>> 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 >>>
Re: [Freesurfer] Tool for incorporating T2-SPACE data in pial surface recons?
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 >>>> >>>>Date: Tuesday, November 20, >>>>2012 5:51 PM >>>>To: Matt Glasser >>>> >>>>Cc: "Watson, Christopher" >>>>, >>>>"Winter, Warren" >>>>, >>>>"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 >>>> 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" >>>> >>>> wrote: >>>> >>>>> Yes, definitely. The >>>>t2-space flair is a big help >>>>> >>>>> >>>>> >>>>> On Nov 20, 2012, at >>>>5:40 PM, "Watson, >>>>Christopher" >>>> >>>>> >>>>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 >>&
Re: [Freesurfer] Tool for incorporating T2-SPACE data in pial surface recons?
n 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 >>>>> >>>>> Date: Tuesday, November 20, >>>>> 2012 5:51 PM >>>>> To: Matt Glasser >>>>> >>>>> Cc: "Watson, Christopher" >>>>> , >>>>> "Winter, Warren" >>>>> , >>>>> "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 >>>>>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" >>>>> >>>>> wrote: >>>>> >>>>>> Yes, definitely. The >>>>> t2-space flair is a big help >>>>>>
Re: [Freesurfer] Tool for incorporating T2-SPACE data in pial surface recons?
Would this new tool also be able to provide a "better" delineation of both pial surface and inner table of the skull (assuming T2 and not FLAIR i.e. hyperintense CSF)) and thus provide the possibility of computing extra-ventricular CSF and thus cerebral atrophy? Some of us would like that I'm sure :-) -roddy -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl Sent: Tuesday, November 20, 2012 2:02 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 > > > ___ 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. UT Southwestern Medical Center The future of medicine, today. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Tool for incorporating T2-SPACE data in pial surface recons?
Yes, although we've only done the pial part so far Bruce On Nov 21, 2012, at 3:06 PM, Roderick McColl wrote: > Would this new tool also be able to provide a "better" delineation of both > pial surface and inner table of the skull > (assuming T2 and not FLAIR i.e. hyperintense CSF)) and thus provide the > possibility of computing extra-ventricular > CSF and thus cerebral atrophy? > Some of us would like that I'm sure :-) > -roddy > > -Original Message- > From: freesurfer-boun...@nmr.mgh.harvard.edu > [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl > Sent: Tuesday, November 20, 2012 2:02 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 >> >> >> > ___ > 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. > > > > > UT Southwestern Medical Center > The future of medicine, today. > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Tool for incorporating T2-SPACE data in pial surface recons?
Thanks for the update - looking forward. Do you have a recommendation on a particular T2 protocol for this purpose? -roddy Possibly Sent from my iPhone On Nov 21, 2012, at 8:46 PM, "Bruce Fischl" wrote: > Yes, although we've only done the pial part so far > Bruce > > > > On Nov 21, 2012, at 3:06 PM, Roderick McColl > wrote: > >> Would this new tool also be able to provide a "better" delineation of both >> pial surface and inner table of the skull >> (assuming T2 and not FLAIR i.e. hyperintense CSF)) and thus provide the >> possibility of computing extra-ventricular >> CSF and thus cerebral atrophy? >> Some of us would like that I'm sure :-) >> -roddy >> >> -Original Message- >> From: freesurfer-boun...@nmr.mgh.harvard.edu >> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl >> Sent: Tuesday, November 20, 2012 2:02 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 >>> >>> >>> >> ___ >> 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. >> >> >> >> >> UT Southwestern Medical Center >> The future of medicine, today. >> >> ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Tool for incorporating T2-SPACE data in pial surface recons?
We use 1mm isotropic t2-space geometry, bandwidth and readout matched to multiecho mprage Cheers Bruce On Nov 22, 2012, at 11:13 AM, Roderick McColl wrote: > Thanks for the update - looking forward. Do you have a recommendation on a > particular T2 protocol for this purpose? > -roddy > > Possibly Sent from my iPhone > > On Nov 21, 2012, at 8:46 PM, "Bruce Fischl" > wrote: > >> Yes, although we've only done the pial part so far >> Bruce >> >> >> >> On Nov 21, 2012, at 3:06 PM, Roderick McColl >> wrote: >> >>> Would this new tool also be able to provide a "better" delineation of both >>> pial surface and inner table of the skull >>> (assuming T2 and not FLAIR i.e. hyperintense CSF)) and thus provide the >>> possibility of computing extra-ventricular >>> CSF and thus cerebral atrophy? >>> Some of us would like that I'm sure :-) >>> -roddy >>> >>> -Original Message- >>> From: freesurfer-boun...@nmr.mgh.harvard.edu >>> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl >>> Sent: Tuesday, November 20, 2012 2:02 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 >>>> >>>> >>>> >>> ___ >>> 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. >>> >>> >>> >>> >>> UT Southwestern Medical Center >>> The future of medicine, today. >>> >>> > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
