Hello All:
I read the paper by Kouwe et al. (2008 NeuroImage 40 p.559).
I was wondering if FreeSurfer (v4.5) is able utilize the multi echo (especially T2-SPACE) sequence in order achieve better segmentation of GM from dura. The paper mentions the code was altered to do this.
If it is possible, is there an additional option or is it able to it by default? I searched the email archive but I couldn't find much information on this topic.
Thanks in advance.
Deniz Ozgen.
Hi Deniz,
yes, it should be in the mris_make_surfaces of that version. You need to run it with -dura memprage_echo%d.mgz 4
where 4 is the # of echoes, and the names would be memprage_echo0.mgz, memprage_echo1.mgz, memprage_echo2.mgz, and memprage_echo3.mgz. These must all be "conformed" to be 256^3 and 1mm isotropic, but *not* scaled, otherwise the T2* info will be lost by the differential scaling. cheers bruce
On Thu, 7 Oct 2010, Deniz Ozgen wrote:
Hello All:
I read the paper by Kouwe et al. (2008 NeuroImage 40 p.559).
I was wondering if FreeSurfer (v4.5) is able utilize the multi echo (especially T2-SPACE) sequence in order achieve better segmentation of GM from dura. The paper mentions the code was altered to do this.
If it is possible, is there an additional option or is it able to it by default? I searched the email archive but I couldn't find much information on this topic.
Thanks in advance.
Deniz Ozgen. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hello, Deniz mentioned "T2-SPACE" rather than the multi-echo MPRAGE (memprage). Can you do something similar using the 3D T2-SPACE?
cheers, -MH
Hi Deniz,
yes, it should be in the mris_make_surfaces of that version. You need to run it with -dura memprage_echo%d.mgz 4
where 4 is the # of echoes, and the names would be memprage_echo0.mgz, memprage_echo1.mgz, memprage_echo2.mgz, and memprage_echo3.mgz. These must all be "conformed" to be 256^3 and 1mm isotropic, but *not* scaled, otherwise the T2* info will be lost by the differential scaling. cheers bruce
On Thu, 7 Oct 2010, Deniz Ozgen wrote:
Hello All:
I read the paper by Kouwe et al. (2008 NeuroImage 40 p.559).
I was wondering if FreeSurfer (v4.5) is able utilize the multi echo (especially T2-SPACE) sequence in order achieve better segmentation of GM from dura. The paper mentions the code was altered to do this.
If it is possible, is there an additional option or is it able to it by default? I searched the email archive but I couldn't find much information on this topic.
Thanks in advance.
Deniz Ozgen. _______________________________________________ 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.
Hi Mike,
not sure, I'd have to look at it. The code wouldn't work as-is, since it uses the ratio of the echoes to get a rough estimate of T2*.
cheers Bruce
On Fri, 8 Oct 2010, Michael Harms wrote:
Hello, Deniz mentioned "T2-SPACE" rather than the multi-echo MPRAGE (memprage). Can you do something similar using the 3D T2-SPACE?
cheers, -MH
Hi Deniz,
yes, it should be in the mris_make_surfaces of that version. You need to run it with -dura memprage_echo%d.mgz 4
where 4 is the # of echoes, and the names would be memprage_echo0.mgz, memprage_echo1.mgz, memprage_echo2.mgz, and memprage_echo3.mgz. These must all be "conformed" to be 256^3 and 1mm isotropic, but *not* scaled, otherwise the T2* info will be lost by the differential scaling. cheers bruce
On Thu, 7 Oct 2010, Deniz Ozgen wrote:
Hello All:
I read the paper by Kouwe et al. (2008 NeuroImage 40 p.559).
I was wondering if FreeSurfer (v4.5) is able utilize the multi echo (especially T2-SPACE) sequence in order achieve better segmentation of GM from dura. The paper mentions the code was altered to do this.
If it is possible, is there an additional option or is it able to it by default? I searched the email archive but I couldn't find much information on this topic.
Thanks in advance.
Deniz Ozgen. _______________________________________________ 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.
freesurfer@nmr.mgh.harvard.edu
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Bruce Fischl -
Deniz Ozgen -
Michael Harms