Re: [Freesurfer] inclusion of both T1 and T2 in a recon-all run

[Bruce Fischl]

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"
 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




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Re: [Freesurfer] inclusion of both T1 and T2 in a recon-all run

[Matt Glasser]

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"
 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
>> 
>>  
>> 
>> 
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>
>
>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
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Re: [Freesurfer] inclusion of both T1 and T2 in a recon-all run

[Bruce Fischl]

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

 


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Re: [Freesurfer] inclusion of both T1 and T2 in a recon-all run

[Harms, Michael]

FWIW, we’ve had good success with including the T2w scan as part of the FS 5.3-HCP release.


cheers,
-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: mha...@wustl.edu






From:  on behalf of "Krieger, Donald N." 
Reply-To: 'Freesurfer support list' 
Date: Tuesday, August 30, 2016 at 9:25 AM
To: 'Freesurfer support list' 
Subject: Re: [Freesurfer] inclusion of both T1 and T2 in a recon-all run








Thank you – very helpful.
 

Best – Don

 



From:
freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@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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Re: [Freesurfer] inclusion of both T1 and T2 in a recon-all run

[Krieger, Donald N.]

Thank you - very helpful.

Best - Don

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@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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Re: [Freesurfer] inclusion of both T1 and T2 in a recon-all run

[Douglas Greve]

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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Re: [Freesurfer] inclusion of both T1 and T2 in a recon-all run

[Douglas Greve]

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



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The information in this e-mail is intended only for the person to whom it is
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[Freesurfer] inclusion of both T1 and T2 in a recon-all run

[Krieger, Donald N.]

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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