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 >> >> ---------------- >> >> 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 > > > -- Shantanu Ghosh, Ph.D. Harvard Medical School & Massachusetts General Hospital Martinos Center for Biomedical Imaging _______________________________________________ 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.
