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!
-- <<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>> 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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