Hi Souheil

I would run the two sets of scans separately; I would expect a T2 bias in the sample if they are run together with ones that have no T2. Perhaps see how T2 images influence the output (maybe have a .fsgd file with T2/noT2 as two levels) to see if there are significnt differences- no?

Hth, shantanu

On Tue, March 19, 2013 1:22 pm, Bruce Fischl wrote:

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)

1. are people who are using this method using 4 echoes of alternating

polarity, or 4 echoes of the same polarity? 2) for some subjects I have also acquired a 3D T2. Any recommendations on using these data together?

Thanks, Souheil

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Souheil Inati, PhD Staff Scientist Functional MRI Facility NIMH/NIH/DHHS souheil.inati@nih.gov 301-402-9409

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