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!
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 <<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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!
-- <<ÿÿ>>~<>~<<ÿÿ>>~<>~<<ÿÿ>>~<>~<<ÿÿ>>~<>~<<ÿÿ>>~<>~<<ÿÿ>>~<>~<<ÿÿ>>~<>~<<ÿÿ>> 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 <<ÿÿ>>~<>~<<ÿÿ>>~<>~<<ÿÿ>>~<>~<<ÿÿ>>~<>~<<ÿÿ>>~<>~<<ÿÿ>>~<>~<<ÿÿ>>~<>~<<ÿÿ>>
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Well our primary reason for using this sequence is to better delineate the amygdala.
On Wed, Feb 2, 2011 at 5:03 PM, Bruce Fischl fischl@nmr.mgh.harvard.eduwrote:
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!
--
<<ÿÿ>>~<>~<<ÿÿ>>~<>~<<ÿÿ>>~<>~<<ÿÿ>>~<>~<<ÿÿ>>~<>~<<ÿÿ>>~<>~<<ÿÿ>>~<>~<<ÿÿ>>
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
<<ÿÿ>>~<>~<<ÿÿ>>~<>~<<ÿÿ>>~<>~<<ÿÿ>>~<>~<<ÿÿ>>~<>~<<ÿÿ>>~<>~<<ÿÿ>>~<>~<<ÿÿ>>
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.
freesurfer@nmr.mgh.harvard.edu
-
Bruce Fischl -
Carl Anderson -
Douglas N Greve