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 >> ______________________________________ >> >> >> >> _______________________________________________ >> 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 mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
