Re: [Freesurfer] using T2* weighted scans to assist with dura stripping in a GE scanner?

2013-05-13 Thread Inati, Souheil (NIH/NIMH) [E]
Hi Matt,

Thanks for the link.

Reading on pages 29-31, I am struck by the complexity of the procedure.  Not to 
say that it doesn't work, or that the single T1w image free-surfer stuff is 
simple :-), on the contrary, it's just that I was expecting to see something 
about an optimization that used both images, rather than something based on the 
T1w image followed by an exclusion criterion based on the T2w image.  Anyway, 
works better than without.

Minor question on the acquisition of the anatomicals:
- Why are you using partial fourier in the read direction?  You're throwing 
away a lot of SNR at the high spatial frequencies, seems a shame to go to 0.7mm 
and then do that.

Cheers,
Souheil

On May 12, 2013, at 10:54 PM, Matt Glasser m...@ma-tea.com wrote:

 This is available online now:
 
 http://authors.elsevier.com/sd/article/S1053811913005053
 
 
 On 5/7/13 3:10 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote:
 
 actually Matt Glasser points out that a brief description is in his paper
 that is coming out soon, and there is also some description in Andre's
 multi-echo mprage paper
 Bruce
 On Tue, 7 May 2013, Inati, Souheil (NIH/NIMH) [E]
 wrote:
 
 thanks :-)
 
 On May 7, 2013, at 3:28 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu
 wrote:
 
 no, of course not :)
 
 On Tue, 7 May 2013, Inati, Souheil (NIH/NIMH) [E]
 wrote:
 
 Hi Bruce,
 
 Out of curiosity and for reference for my users, do you have a paper
 on the T2 or FLAIR assisted segmentation?
 
 Cheers,
 Souheil
 
 -
 
 Souheil Inati, PhD
 Staff Scientist
 FMRI Facility
 NIMH/NIH/DHHS
 souheil.in...@nih.govmailto:souheil.in...@nih.gov
 
 
 
 
 On May 7, 2013, at 2:24 PM, Bruce Fischl
 fis...@nmr.mgh.harvard.edumailto:fis...@nmr.mgh.harvard.edu wrote:
 
 Hi Katie
 
 I'm really not sure. These days I would recommend a highres (e.g. 1mm
 isotropic) FLAIR if you can get one, or T2 if not. The T2* can help,
 but
 it's pretty noisy in brain.
 
 cheers
 Bruce
 
 On Tue, 7 May 2013, Katie Surrence wrote:
 
 Dear Freesurfer gurus,
 
 At the course, André van der Kouwe mentioned in his morphometry
 methods talk that T2* weighted contrast from
 MEMPRAGE could be used to further seperate dura from cortex, as also
 discussed in this paper:
 http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2408694/.  We have a GE
 scanner in our lab.  The internet suggests
 that a Multi-echo FSPGR/FGRE exists.  Would this be the analog?
 Would it work the same way?  Could you also
 use these images with the mris_make_surfaces command?
 
 Thanks very much for your insight -- and I enjoyed the course!
 
 /Katie Surrence
 
 --
 Research Coordinator
 Social Cognition Laboratory
 New York State Psychiatric Institute
 
 ___
 Freesurfer mailing list
 Freesurfer@nmr.mgh.harvard.edumailto: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
 
 
 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] using T2* weighted scans to assist with dura stripping in a GE scanner?

2013-05-13 Thread Matt Glasser
Gordon Xu who helped us set up the protocol reminded me of the following:

The main benefit of the readout PF is to reduce echo spacing, hence less
blurring in the slice direction. The side benefit is that it also reduces
the minimum TE, hence less dropout. However, you do give up some SNR at
the high spatial frequency as Souheil mentioned. There are two senarios of
this, a) the SNR is adequate, you only lose some SNR due to less sampling,
b) if the SNR is borderline or worse, in addition to losing SNR you also
lose some spatial resolution in the readout direction as the other side of
the high spatial frequency k-space is less reliable.

I remember we did pilot acquisition with and without asymmetric echo in
two subjects. You looked at the images and you either liked the one with
asymmetric echo because of less blurring or at least indifferent between
the two. So I assume with the Siemens 32ch coil we are in senario a)
above.


If I had to guess, we probably went with the readout partial fourier to
reduce the dropout regions in the gradient echo MPRAGE and didn't see an
obvious loss in resolution.

Peace,

Matt.

On 5/13/13 1:03 PM, Inati, Souheil (NIH/NIMH) [E]
souheil.in...@nih.gov wrote:

Hi Matt,

Thanks for the link.

Reading on pages 29-31, I am struck by the complexity of the procedure.
Not to say that it doesn't work, or that the single T1w image free-surfer
stuff is simple :-), on the contrary, it's just that I was expecting to
see something about an optimization that used both images, rather than
something based on the T1w image followed by an exclusion criterion based
on the T2w image.  Anyway, works better than without.

Minor question on the acquisition of the anatomicals:
- Why are you using partial fourier in the read direction?  You're
throwing away a lot of SNR at the high spatial frequencies, seems a shame
to go to 0.7mm and then do that.

Cheers,
Souheil

On May 12, 2013, at 10:54 PM, Matt Glasser m...@ma-tea.com wrote:

 This is available online now:
 
 http://authors.elsevier.com/sd/article/S1053811913005053
 
 
 On 5/7/13 3:10 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote:
 
 actually Matt Glasser points out that a brief description is in his
paper
 that is coming out soon, and there is also some description in Andre's
 multi-echo mprage paper
 Bruce
 On Tue, 7 May 2013, Inati, Souheil (NIH/NIMH) [E]
 wrote:
 
 thanks :-)
 
 On May 7, 2013, at 3:28 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu
 wrote:
 
 no, of course not :)
 
 On Tue, 7 May 2013, Inati, Souheil (NIH/NIMH) [E]
 wrote:
 
 Hi Bruce,
 
 Out of curiosity and for reference for my users, do you have a paper
 on the T2 or FLAIR assisted segmentation?
 
 Cheers,
 Souheil
 
 -
 
 Souheil Inati, PhD
 Staff Scientist
 FMRI Facility
 NIMH/NIH/DHHS
 souheil.in...@nih.govmailto:souheil.in...@nih.gov
 
 
 
 
 On May 7, 2013, at 2:24 PM, Bruce Fischl
 fis...@nmr.mgh.harvard.edumailto:fis...@nmr.mgh.harvard.edu
wrote:
 
 Hi Katie
 
 I'm really not sure. These days I would recommend a highres (e.g.
1mm
 isotropic) FLAIR if you can get one, or T2 if not. The T2* can help,
 but
 it's pretty noisy in brain.
 
 cheers
 Bruce
 
 On Tue, 7 May 2013, Katie Surrence wrote:
 
 Dear Freesurfer gurus,
 
 At the course, André van der Kouwe mentioned in his morphometry
 methods talk that T2* weighted contrast from
 MEMPRAGE could be used to further seperate dura from cortex, as also
 discussed in this paper:
 http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2408694/.  We have a GE
 scanner in our lab.  The internet suggests
 that a Multi-echo FSPGR/FGRE exists.  Would this be the analog?
 Would it work the same way?  Could you also
 use these images with the mris_make_surfaces command?
 
 Thanks very much for your insight -- and I enjoyed the course!
 
 /Katie Surrence
 
 --
 Research Coordinator
 Social Cognition Laboratory
 New York State Psychiatric Institute
 
 ___
 Freesurfer mailing list
 
Freesurfer@nmr.mgh.harvard.edumailto: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
 
 
 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
 

Re: [Freesurfer] using T2* weighted scans to assist with dura stripping in a GE scanner?

2013-05-12 Thread Matt Glasser
This is available online now:

http://authors.elsevier.com/sd/article/S1053811913005053


On 5/7/13 3:10 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote:

actually Matt Glasser points out that a brief description is in his paper
that is coming out soon, and there is also some description in Andre's
multi-echo mprage paper
Bruce
On Tue, 7 May 2013, Inati, Souheil (NIH/NIMH) [E]
wrote:

 thanks :-)

 On May 7, 2013, at 3:28 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu
wrote:

 no, of course not :)

 On Tue, 7 May 2013, Inati, Souheil (NIH/NIMH) [E]
 wrote:

 Hi Bruce,

 Out of curiosity and for reference for my users, do you have a paper
on the T2 or FLAIR assisted segmentation?

 Cheers,
 Souheil

 -

 Souheil Inati, PhD
 Staff Scientist
 FMRI Facility
 NIMH/NIH/DHHS
 souheil.in...@nih.govmailto:souheil.in...@nih.gov




 On May 7, 2013, at 2:24 PM, Bruce Fischl
fis...@nmr.mgh.harvard.edumailto:fis...@nmr.mgh.harvard.edu wrote:

 Hi Katie

 I'm really not sure. These days I would recommend a highres (e.g. 1mm
 isotropic) FLAIR if you can get one, or T2 if not. The T2* can help,
but
 it's pretty noisy in brain.

 cheers
 Bruce

 On Tue, 7 May 2013, Katie Surrence wrote:

 Dear Freesurfer gurus,

 At the course, André van der Kouwe mentioned in his morphometry
methods talk that T2* weighted contrast from
 MEMPRAGE could be used to further seperate dura from cortex, as also
discussed in this paper:
 http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2408694/.  We have a GE
scanner in our lab.  The internet suggests
 that a Multi-echo FSPGR/FGRE exists.  Would this be the analog?
Would it work the same way?  Could you also
 use these images with the mris_make_surfaces command?

 Thanks very much for your insight -- and I enjoyed the course!

 /Katie Surrence

 --
 Research Coordinator
 Social Cognition Laboratory
 New York State Psychiatric Institute

 ___
 Freesurfer mailing list
 Freesurfer@nmr.mgh.harvard.edumailto: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


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] using T2* weighted scans to assist with dura stripping in a GE scanner?

2013-05-10 Thread Katie Surrence
Thanks very much for your response, Bruce.  We already collect T2 in our
scanner -- not sure about FLAIR.  Is there a way for them to work
analogously with the mri_make_surfaces command (as outlined here)?:

FreeSurfer command to correct dura:
mris_make_surfaces–dura filename_%d.mgz
-${lastecho}
-aseg aseg.auto.mgz
-mgz
-sdir ${SUBJECTS_DIR}
-output _dura_1and${lastecho}
$({target} ${hemi}
where filename_%d.mgz refers to the four separated echoes of the MEMPRAGE
and lastecho = 4
Generates:
lh.pial_dura_1and4, rh.pial_dura_1and4,
lh.white_dura_1and4, rh.white_dura_1and4


Thanks again for your help!


On Tue, May 7, 2013 at 2:24 PM, Bruce Fischl fis...@nmr.mgh.harvard.eduwrote:

 Hi Katie

 I'm really not sure. These days I would recommend a highres (e.g. 1mm
 isotropic) FLAIR if you can get one, or T2 if not. The T2* can help, but
 it's pretty noisy in brain.

 cheers
 Bruce


 On Tue, 7 May 2013, Katie Surrence wrote:

  Dear Freesurfer gurus,

 At the course, André van der Kouwe mentioned in his morphometry methods
 talk that T2* weighted contrast from
 MEMPRAGE could be used to further seperate dura from cortex, as also
 discussed in this paper:
 http://www.ncbi.nlm.nih.gov/**pmc/articles/PMC2408694/http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2408694/.
 We have a GE scanner in our lab.  The internet suggests
 that a Multi-echo FSPGR/FGRE exists.  Would this be the analog?  Would it
 work the same way?  Could you also
 use these images with the mris_make_surfaces command?

 Thanks very much for your insight -- and I enjoyed the course!

 /Katie Surrence

 --
 Research Coordinator
 Social Cognition Laboratory
 New York State Psychiatric Institute




 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.




-- 
Research Coordinator
Social Cognition Laboratory
New York State Psychiatric Institute
___
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] using T2* weighted scans to assist with dura stripping in a GE scanner?

2013-05-07 Thread Bruce Fischl

Hi Katie

I'm really not sure. These days I would recommend a highres (e.g. 1mm 
isotropic) FLAIR if you can get one, or T2 if not. The T2* can help, but 
it's pretty noisy in brain.


cheers
Bruce

On Tue, 7 May 2013, Katie Surrence wrote:


Dear Freesurfer gurus,

At the course, André van der Kouwe mentioned in his morphometry methods talk 
that T2* weighted contrast from
MEMPRAGE could be used to further seperate dura from cortex, as also discussed 
in this paper:
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2408694/.  We have a GE scanner in 
our lab.  The internet suggests
that a Multi-echo FSPGR/FGRE exists.  Would this be the analog?  Would it work 
the same way?  Could you also
use these images with the mris_make_surfaces command?

Thanks very much for your insight -- and I enjoyed the course!

/Katie Surrence

--
Research Coordinator
Social Cognition Laboratory
New York State Psychiatric Institute

___
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] using T2* weighted scans to assist with dura stripping in a GE scanner?

2013-05-07 Thread Inati, Souheil (NIH/NIMH) [E]
Hi Bruce,

Out of curiosity and for reference for my users, do you have a paper on the T2 
or FLAIR assisted segmentation?

Cheers,
Souheil

-

Souheil Inati, PhD
Staff Scientist
FMRI Facility
NIMH/NIH/DHHS
souheil.in...@nih.govmailto:souheil.in...@nih.gov




On May 7, 2013, at 2:24 PM, Bruce Fischl 
fis...@nmr.mgh.harvard.edumailto:fis...@nmr.mgh.harvard.edu wrote:

Hi Katie

I'm really not sure. These days I would recommend a highres (e.g. 1mm
isotropic) FLAIR if you can get one, or T2 if not. The T2* can help, but
it's pretty noisy in brain.

cheers
Bruce

On Tue, 7 May 2013, Katie Surrence wrote:

Dear Freesurfer gurus,

At the course, André van der Kouwe mentioned in his morphometry methods talk 
that T2* weighted contrast from
MEMPRAGE could be used to further seperate dura from cortex, as also discussed 
in this paper:
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2408694/.  We have a GE scanner in 
our lab.  The internet suggests
that a Multi-echo FSPGR/FGRE exists.  Would this be the analog?  Would it work 
the same way?  Could you also
use these images with the mris_make_surfaces command?

Thanks very much for your insight -- and I enjoyed the course!

/Katie Surrence

--
Research Coordinator
Social Cognition Laboratory
New York State Psychiatric Institute

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edumailto: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] using T2* weighted scans to assist with dura stripping in a GE scanner?

2013-05-07 Thread Bruce Fischl

no, of course not :)

On Tue, 7 May 2013, Inati, Souheil (NIH/NIMH) [E] 
wrote:



Hi Bruce,

Out of curiosity and for reference for my users, do you have a paper on the T2 
or FLAIR assisted segmentation?

Cheers,
Souheil

-

Souheil Inati, PhD
Staff Scientist
FMRI Facility
NIMH/NIH/DHHS
souheil.in...@nih.govmailto:souheil.in...@nih.gov




On May 7, 2013, at 2:24 PM, Bruce Fischl 
fis...@nmr.mgh.harvard.edumailto:fis...@nmr.mgh.harvard.edu wrote:

Hi Katie

I'm really not sure. These days I would recommend a highres (e.g. 1mm
isotropic) FLAIR if you can get one, or T2 if not. The T2* can help, but
it's pretty noisy in brain.

cheers
Bruce

On Tue, 7 May 2013, Katie Surrence wrote:

Dear Freesurfer gurus,

At the course, André van der Kouwe mentioned in his morphometry methods talk 
that T2* weighted contrast from
MEMPRAGE could be used to further seperate dura from cortex, as also discussed 
in this paper:
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2408694/.  We have a GE scanner in 
our lab.  The internet suggests
that a Multi-echo FSPGR/FGRE exists.  Would this be the analog?  Would it work 
the same way?  Could you also
use these images with the mris_make_surfaces command?

Thanks very much for your insight -- and I enjoyed the course!

/Katie Surrence

--
Research Coordinator
Social Cognition Laboratory
New York State Psychiatric Institute

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edumailto: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


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] using T2* weighted scans to assist with dura stripping in a GE scanner?

2013-05-07 Thread Inati, Souheil (NIH/NIMH) [E]
thanks :-)

On May 7, 2013, at 3:28 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote:

 no, of course not :)
 
 On Tue, 7 May 2013, Inati, Souheil (NIH/NIMH) [E] 
 wrote:
 
 Hi Bruce,
 
 Out of curiosity and for reference for my users, do you have a paper on the 
 T2 or FLAIR assisted segmentation?
 
 Cheers,
 Souheil
 
 -
 
 Souheil Inati, PhD
 Staff Scientist
 FMRI Facility
 NIMH/NIH/DHHS
 souheil.in...@nih.govmailto:souheil.in...@nih.gov
 
 
 
 
 On May 7, 2013, at 2:24 PM, Bruce Fischl 
 fis...@nmr.mgh.harvard.edumailto:fis...@nmr.mgh.harvard.edu wrote:
 
 Hi Katie
 
 I'm really not sure. These days I would recommend a highres (e.g. 1mm
 isotropic) FLAIR if you can get one, or T2 if not. The T2* can help, but
 it's pretty noisy in brain.
 
 cheers
 Bruce
 
 On Tue, 7 May 2013, Katie Surrence wrote:
 
 Dear Freesurfer gurus,
 
 At the course, André van der Kouwe mentioned in his morphometry methods talk 
 that T2* weighted contrast from
 MEMPRAGE could be used to further seperate dura from cortex, as also 
 discussed in this paper:
 http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2408694/.  We have a GE scanner 
 in our lab.  The internet suggests
 that a Multi-echo FSPGR/FGRE exists.  Would this be the analog?  Would it 
 work the same way?  Could you also
 use these images with the mris_make_surfaces command?
 
 Thanks very much for your insight -- and I enjoyed the course!
 
 /Katie Surrence
 
 --
 Research Coordinator
 Social Cognition Laboratory
 New York State Psychiatric Institute
 
 ___
 Freesurfer mailing list
 Freesurfer@nmr.mgh.harvard.edumailto: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] using T2* weighted scans to assist with dura stripping in a GE scanner?

2013-05-07 Thread Bruce Fischl
actually Matt Glasser points out that a brief description is in his paper 
that is coming out soon, and there is also some description in Andre's 
multi-echo mprage paper

Bruce
On Tue, 7 May 2013, Inati, Souheil (NIH/NIMH) [E] 
wrote:



thanks :-)

On May 7, 2013, at 3:28 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote:


no, of course not :)

On Tue, 7 May 2013, Inati, Souheil (NIH/NIMH) [E]
wrote:


Hi Bruce,

Out of curiosity and for reference for my users, do you have a paper on the T2 
or FLAIR assisted segmentation?

Cheers,
Souheil

-

Souheil Inati, PhD
Staff Scientist
FMRI Facility
NIMH/NIH/DHHS
souheil.in...@nih.govmailto:souheil.in...@nih.gov




On May 7, 2013, at 2:24 PM, Bruce Fischl 
fis...@nmr.mgh.harvard.edumailto:fis...@nmr.mgh.harvard.edu wrote:

Hi Katie

I'm really not sure. These days I would recommend a highres (e.g. 1mm
isotropic) FLAIR if you can get one, or T2 if not. The T2* can help, but
it's pretty noisy in brain.

cheers
Bruce

On Tue, 7 May 2013, Katie Surrence wrote:

Dear Freesurfer gurus,

At the course, André van der Kouwe mentioned in his morphometry methods talk 
that T2* weighted contrast from
MEMPRAGE could be used to further seperate dura from cortex, as also discussed 
in this paper:
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2408694/.  We have a GE scanner in 
our lab.  The internet suggests
that a Multi-echo FSPGR/FGRE exists.  Would this be the analog?  Would it work 
the same way?  Could you also
use these images with the mris_make_surfaces command?

Thanks very much for your insight -- and I enjoyed the course!

/Katie Surrence

--
Research Coordinator
Social Cognition Laboratory
New York State Psychiatric Institute

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edumailto: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


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.