Hi Katie,
yes, give mris_make_surfaces the -T2dura <T2/FLAIR volume name) command
after recon-all has completed.
cheers
Bruce
On Fri, 10 May 2013, Katie Surrence wrote:
Thanks very much for your response, Bruce. We already collect T2 in our
scanner -- not sure about FLAIR. Is there a way for them to work
analogously with the mri_make_surfaces command (as outlined here)?:
FreeSurfer command to correct dura:
mris_make_surfaces –dura filename_%d.mgz
-${lastecho}
-aseg aseg.auto.mgz
-mgz
-sdir ${SUBJECTS_DIR}
-output _dura_1and${lastecho}
$({target} ${hemi}
where filename_%d.mgz refers to the four separated echoes of the MEMPRAGE
and lastecho = 4
Generates:
lh.pial_dura_1and4, rh.pial_dura_1and4,
lh.white_dura_1and4, rh.white_dura_1and4
Thanks again for your help!
On Tue, May 7, 2013 at 2:24 PM, Bruce Fischl <fis...@nmr.mgh.harvard.edu>
wrote:
Hi Katie
I'm really not sure. These days I would recommend a highres
(e.g. 1mm isotropic) FLAIR if you can get one, or T2 if not. The
T2* can help, but it's pretty noisy in brain.
cheers
Bruce
On Tue, 7 May 2013, Katie Surrence wrote:
Dear Freesurfer gurus,
At the course, André van der Kouwe mentioned in his
morphometry methods talk that T2* weighted contrast
from
MEMPRAGE could be used to further seperate dura from
cortex, as also discussed in this paper:
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2408694/.
We have a GE scanner in our lab. The internet
suggests
that a Multi-echo FSPGR/FGRE exists. Would this be
the analog? Would it work the same way? Could you
also
use these images with the mris_make_surfaces
command?
Thanks very much for your insight -- and I enjoyed
the course!
/Katie Surrence
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