Dear list:
What are the advantages of including a T2 scan when running recon-all -all ? Which results can it effect and to what extent? And how sensitive is freesurfer to artifacts in the T2 scan? Is there a good reference for this/
Thanks and best - Don
Hi Don,
the T2 stream is a work-in-progress, so we don't have a lot of these answers. In theory, a T2 will allow better placement of the pial surface allowing it to better exclude dura. No publication on this yet.
doug
On 8/30/16 10:12 AM, Krieger, Donald N. wrote:
Dear list:
What are the advantages of including a T2 scan when running recon-all –all ?
Which results can it effect and to what extent?
And how sensitive is freesurfer to artifacts in the T2 scan?
Is there a good reference for this/
Thanks and best - Don
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
ps. The 5.3 version is pretty buggy, so I'd wait until 6.0 to test it out
On 8/30/16 10:12 AM, Krieger, Donald N. wrote:
Dear list:
What are the advantages of including a T2 scan when running recon-all –all ?
Which results can it effect and to what extent?
And how sensitive is freesurfer to artifacts in the T2 scan?
Is there a good reference for this/
Thanks and best - Don
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Thank you - very helpful.
Best - Don
From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Douglas Greve Sent: Tuesday, August 30, 2016 10:23 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] inclusion of both T1 and T2 in a recon-all run
ps. The 5.3 version is pretty buggy, so I'd wait until 6.0 to test it out
On 8/30/16 10:12 AM, Krieger, Donald N. wrote: Dear list:
What are the advantages of including a T2 scan when running recon-all -all ? Which results can it effect and to what extent? And how sensitive is freesurfer to artifacts in the T2 scan? Is there a good reference for this/
Thanks and best - Don
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Hi Don
the T2 or FLAIR helps us avoid dura. It is still a beta version though as we don't have a ton of experience with it, and no, there is no reference for it yet (or maybe ever) :) Bruce
On Tue, 30 Aug 2016, Krieger, Donald N. wrote:
Dear list:
What are the advantages of including a T2 scan when running recon-all –all ?
Which results can it effect and to what extent?
And how sensitive is freesurfer to artifacts in the T2 scan?
Is there a good reference for this/
Thanks and best - Don
Sure there¹s a publication. See Figure 14:
http://www.sciencedirect.com/science/article/pii/S1053811913005053
Peace,
Matt.
On 8/30/16, 10:21 AM, "Bruce Fischl" <freesurfer-bounces@nmr.mgh.harvard.edu on behalf of fischl@nmr.mgh.harvard.edu> wrote:
Hi Don
the T2 or FLAIR helps us avoid dura. It is still a beta version though as we don't have a ton of experience with it, and no, there is no reference for it yet (or maybe ever) :) Bruce
On Tue, 30 Aug 2016, Krieger, Donald N. wrote:
Dear list:
What are the advantages of including a T2 scan when running recon-all all ?
Which results can it effect and to what extent?
And how sensitive is freesurfer to artifacts in the T2 scan?
Is there a good reference for this/
Thanks and best - Don
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.
Hi Matt
I don't think that counts as a methods paper for the T2-based deformation. There is no validation or comparison with other methods in it, and really not enough detail to replicate what we did.
cheers Bruce On Tue, 30 Aug 2016, Matt Glasser wrote:
Sure there¹s a publication. See Figure 14:
http://www.sciencedirect.com/science/article/pii/S1053811913005053
Peace,
Matt.
On 8/30/16, 10:21 AM, "Bruce Fischl" <freesurfer-bounces@nmr.mgh.harvard.edu on behalf of fischl@nmr.mgh.harvard.edu> wrote:
Hi Don
the T2 or FLAIR helps us avoid dura. It is still a beta version though as we don't have a ton of experience with it, and no, there is no reference for it yet (or maybe ever) :) Bruce
On Tue, 30 Aug 2016, Krieger, Donald N. wrote:
Dear list:
What are the advantages of including a T2 scan when running recon-all all ?
Which results can it effect and to what extent?
And how sensitive is freesurfer to artifacts in the T2 scan?
Is there a good reference for this/
Thanks and best - Don
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
actually I had forgotten that we described the basic surface deformation to avoid dura in Andre's paper, which is what I first wrote it for:
2008 Brain morphometry with multiecho MPRAGE. van der Kouwe, Andre J W; Benner, Thomas; Salat, David H and Fischl, Bruce NeuroImage, 2008.
On Tue, 30 Aug 2016, Bruce Fischl wrote:
Hi Matt
I don't think that counts as a methods paper for the T2-based deformation. There is no validation or comparison with other methods in it, and really not enough detail to replicate what we did.
cheers Bruce On Tue, 30 Aug 2016, Matt Glasser wrote:
Sure there¹s a publication. See Figure 14:
http://www.sciencedirect.com/science/article/pii/S1053811913005053
Peace,
Matt.
On 8/30/16, 10:21 AM, "Bruce Fischl" <freesurfer-bounces@nmr.mgh.harvard.edu on behalf of fischl@nmr.mgh.harvard.edu> wrote:
Hi Don
the T2 or FLAIR helps us avoid dura. It is still a beta version though as we don't have a ton of experience with it, and no, there is no reference for it yet (or maybe ever) :) Bruce
On Tue, 30 Aug 2016, Krieger, Donald N. wrote:
Dear list:
What are the advantages of including a T2 scan when running recon-all all ?
Which results can it effect and to what extent?
And how sensitive is freesurfer to artifacts in the T2 scan?
Is there a good reference for this/
Thanks and best - Don
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@nmr.mgh.harvard.edu
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Bruce Fischl -
Douglas Greve -
Harms, Michael -
Krieger, Donald N. -
Matt Glasser