On Wed, Feb 2, 2011 at 5:03 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote:

what do you want to do with the echoes?

On Wed, 2 Feb 2011, Douglas N Greve wrote:

Hi Carl, you're probably better off taking the RMS (root-mean-square) of
the echoes rather than averaging them together. Our scanner outputs
these in addition to the echoes, but they are easy to compute with calls
to mri_concat.

doug

btw, you can't really have motion between the echoes. All four echoes
for each line of k-space are acquired within 20ms of each other.

Carl Anderson wrote:

Dear Freesurfer,

I am concerned that I may not be processing the MEMPRAGE images to
full take advantage of the T2* info in the multi-echos.

I have been separating each echo as 001.mgz, 002.mgz, 003.mgz &
004.mgz when using recon-all. This works well if motion exists in any
of the individual echos.

However of late, I have noticed a that a reference was made to the
problem of losing T2* info by differential scaling in the archive if a
particular file format "memprage_echo0.mgz" was not used.

Here is the link to the archive note:
http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg15303.html

It has been hard to identify a difference between our standard MPRAGE
images and the MEMPRAGE images (we currently collect both on our
Siemens 3T 32 channel system).

Am I processing the MEMPRAGE correctly?

Thanks!

--
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Carl M. Anderson, Ph.D. (mail stop 204)
Assistant Professor of Psychiatry,
Harvard Medical School &
The Neuroimaging Center,
McLean Hospital 115 Mill St. Belmont, MA 02478
Ph: 617-855-2972; Fax: 617-855-2770
e-mail: remfract@gmail.com <mailto:remfract@gmail.com>;
carl_anderson@hms.harvard.edu <mailto:carl_anderson@hms.harvard.edu>
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