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 fischl@nmr.mgh.harvard.eduwrote:
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/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
-- Research Coordinator Social Cognition Laboratory New York State Psychiatric Institute
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