Hi Souheil
we usually compute the RMS across echoes and give that to recon-all as a normal mprage. It's a reasonable (although of course not optimal) weighting since the earlier echoes have more signal and more contrast.
For the T2s, there's a new post-hoc procedure for deformaing the surfaces to match them (-T2pial or something like that in recon-all)
cheers Bruce
On Tue, 19 Mar 2013, Inati, Souheil (NIH/NIMH) [E] wrote:
Hi All,
I have some multi-echo mprage images from a sequence and protocol set up to emulate Andre's 2008 paper. What's are the "best-practices" for using data from this type of sequence in Freesurfer?
Related side questions: I have used the suggested morphometry protocols on the FS wiki (1mm iso resolution, same FOV, bandwidth matched, etc)
- are people who are using this method using 4 echoes of alternating polarity, or 4 echoes of the same polarity?
- for some subjects I have also acquired a 3D T2. Any recommendations on using these data together?
Thanks, Souheil
Souheil Inati, PhD Staff Scientist Functional MRI Facility NIMH/NIH/DHHS souheil.inati@nih.gov 301-402-9409
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