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

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

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

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

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

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

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

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

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

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

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

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

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

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