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 > > ---------------- > > Souheil Inati, PhD > Staff Scientist > Functional MRI Facility > NIMH/NIH/DHHS > souheil.in...@nih.gov > 301-402-9409 > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > _______________________________________________ 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.
