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
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
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
_______________________________________________ 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.
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
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.
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
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
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
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
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 > > >
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
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. Â Two images with roughly the same contrast won't work for the ratio method. Â 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 >>> >>> >>> >> _______________________________________________ >> 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
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 >>> >>> >>> >> _______________________________________________ >> 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
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 >>> >>> >>> >> _______________________________________________ >> 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
thanks matt and bruce. this is very helpful.
cheers,
satra
On Tue, Nov 20, 2012 at 7:53 PM, Bruce Fischl fischl@nmr.mgh.harvard.eduwrote:
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.eduChristopher.Watson@childrens.harvard.edu
,
"Winter, Warren" <Warren.Winter@childrens.**harvard.eduWarren.Winter@childrens.harvard.edu
,
"freesurfer@nmr.mgh.harvard.**edu freesurfer@nmr.mgh.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<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.edufreesurfer-bounces@nmr.mgh.harvard.edu >>[freesurfer-bounces@nmr.mgh.**harvard.edufreesurfer-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/** freesurferhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> >>> >> ______________________________**_________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/** freesurferhttps://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/**compliancelinehttp://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 Freesurfer@nmr.mgh.harvard.edu >https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurferhttps://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<https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>
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 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    >>>    >>>    >>>    >> _______________________________________________    >> 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
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" fischl@nmr.mgh.harvard.edu 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 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 >>> >>> >>> >> _______________________________________________ >> 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. >> >> >> >
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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 matt@ma-tea.com 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" fischl@nmr.mgh.harvard.edu 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 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 helpOn 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 aprotocol?
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 PMTo: Winter, Warren Cc:
freesurfer@nmr.mgh.harvard.eduSubject: Re:
[Freesurfer] Tool for incorporating T2-SPACE data in pialsurface recons?
Hi Warren
yes, it will be part
of the upcoming 5.2 release, hopefully in Dec. Itwill 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 underdevelopment some
scripts designed to utilize T2-SPACE images for betterpial surface
reconstruction in the presence of dura -- I was justwondering if any of
that is ready for trial?Thanks!
Warren
-- Warren Winter Research
CoordinatorBoston Children's
HospitalSheridan Laboratory
of Cognitive NeuroscienceDivision of
Developmental Medicine1 Autumn Street, AU
650Boston, MA 02215 857-218-5224
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The information in
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believe this e-mail was sent to you in error and thee-mail contains patient
information, please contact the Partners ComplianceHelpLine at
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Hi Bruce, How are you matching the BW for T2-SPACE vs. MPRAGE -- the former typically has a BW around 700+ Hz/Px, while the latter is typically around 200 Hz/Px.
thanks, -MH
We use Andre's multiecho mprage
On Nov 20, 2012, at 10:31 PM, Michael Harms mharms@conte.wustl.edu wrote:
Hi Bruce, How are you matching the BW for T2-SPACE vs. MPRAGE -- the former typically has a BW around 700+ Hz/Px, while the latter is typically around 200 Hz/Px.
thanks, -MH
-- Michael Harms, Ph.D.
Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134 660 South Euclid Ave. Tel: 314-747-6173 St. Louis, MO 63110 Email: mharms@wustl.edu
On 11/20/12 8:11 PM, "Bruce Fischl" fischl@nmr.mgh.harvard.edu wrote:
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 matt@ma-tea.com 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" fischl@nmr.mgh.harvard.edu 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 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 helpOn 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-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
>> >> >> >
_______________________________________________> Freesurfer mailing
list>
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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.> > >
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listFreesurfer@nmr.mgh.harvard.edu
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_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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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-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@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.
Yes, although we've only done the pial part so far Bruce
On Nov 21, 2012, at 3:06 PM, Roderick McColl Roderick.McColl@utsouthwestern.edu 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-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@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.
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" fischl@nmr.mgh.harvard.edu wrote:
Yes, although we've only done the pial part so far Bruce
On Nov 21, 2012, at 3:06 PM, Roderick McColl Roderick.McColl@utsouthwestern.edu 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-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@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.
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 Roderick.McColl@utsouthwestern.edu 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" fischl@nmr.mgh.harvard.edu wrote:
Yes, although we've only done the pial part so far Bruce
On Nov 21, 2012, at 3:06 PM, Roderick McColl Roderick.McColl@utsouthwestern.edu 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-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@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@nmr.mgh.harvard.edu
-
Bruce Fischl -
Matt Glasser -
Michael Harms -
Roderick McColl -
Satrajit Ghosh -
Watson, Christopher -
Winter, Warren