You can run this command to incorporate the T2 image:
recon-all -i /path/to/MEMPRAGE -T2 /path/to/T2 -T2pial -s subject_name -all
After completing, this will produce ?h.pial which use the T2 image, and
?h.woT2.pial which are the same pial surfaces as recon-all without T2 input.
Best,
Lee
On Tue, 18 Aug 2015, Bruce Fischl wrote:
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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