no, there is a post-hoc recon-all target you can use. -T2 or -T2pial or
something. Sorry, I don't remember, maybe someone else can fill in the
details
Bruce
On Tue, 18 Aug 2015, John Pyles wrote:
Hi Bruce,
Thanks so much! We do have a bandwidth matched T2-space. So should that be fed
into recon-all at the same time as the MEMPRAGE as a second series?
best,
John
On 8/18/15, at Tue,Aug 18 - 8:32:00 PM, Bruce Fischl
<fis...@nmr.mgh.harvard.edu> wrote:
Hi John
the MEFLASH never achieved as good cortical contrast as the memprage, so for
cotical stuff we still recomment memprage. And yes, feeding the RMS to
recon-all will be fine. If you can get a readout/bandwidth matched T2-space or
FLAIR that can be a pretty big help as well for avoiding dura
cheers
Bruce
On Tue, 18 Aug 2015, John Pyles wrote:
Hi all,
We have recently installed the FreeSurfer suggested morphometry sequences on
our Siemens Verio 3T. Specifically, the multiecho MPRAGE (MEMPRAGE), and
multiecho FLASH (MEFLASH). Our goal is to get the best FreeSurfer
reconstruction results possible for use with fMRI surface analyses, diffusion
imaging, and other purposes. For the current project, scan time is not at a
premium since we have 60-90min budgeted for anatomical and diffusion weighted
scans. We’re just looking for the best results.
However, after looking through the wiki and email archives, I’m having a hard
time figuring out what the most up to date recommendations are for what
sequences to use and how to use them with recon-all.
Some specific questions:
1) The original 2009 "Suggested Morphometry Protocols” document, the MEFLASH
seems to be recommended as the best sequence to use for whole-brain segmentation.
But other more recent posts to the email list suggest using MEMPRAGE as the default
protocol. We also have a very nice T2-SPACE protocol we’ve been running. What is the
current recommendation?
2) Is the procedure for using MEMPRAGE with recon-all to just input the RMS
scan and not the 4 different echos?
3) Is it possible to use the MEFLASH scans with recon-all? If so, how are they
input and is processing of the two different echo time scans required before
running recon-all? The wiki entry on MEF is from 2008, so I’m not sure what’s
happened since then.
4) What is the current recommendation on using the -3T and -mprage flags with
recon-all?
5) Since we are scanning on a Siemens Verio instead of the TIM Trio scanners I
believe the sequences were developed on, we have had to modify some protocol
parameters. If anyone has been successfully scanning MEFLASH and/or MEMPRAGE on
a Verio or possibly Skyra and has good parameters to use that would be great.
Our test scans look good, but there is always room for improvement.
6) Finally, is 1mm isovoxel still recommended? Or should we try to push the
resolution below 1mm?
Thanks so much in advance for any advice!
best regards,
John
______________________________________
John Pyles, Ph.D.
Research Scientist
Center for the Neural Basis of Cognition
Department of Psychology
Carnegie Mellon University
email: jpy...@cmu.edu
phone: 206.552.0107
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