Thanks Bruce! That’s really good to know. So therefore, no need to have a “compromise” set of echo images for dura correction if I’m not feeding both inputs to recon-all? Would it make sense to run both days separately and just average thickness values between ROIs to reach a single value for each subject?
I guess this question is slightly complicated by having functional data on both days as well. I was debating which structural scan (post-freesurfer) to use as my registration base for the functional data. It seems I have two options: use the scan collected the same day as the functional — or use a single structural for both days (hence the impulse to feed both scans to a single recon-all. I suppose a third option is just pick the scan with best quality and go with that for everything. Do you have a gut feeling on which is the better strategy? Best, Jared > Hi Jared > > it's really an empirical question. With high quality data we have found > that adding scans doesn't help CNR very much (it reduced the N but the > blurring induced by differential distortion also reduces the C). If your > scans are noisy it might be worth it, but it really depends on the > acquisition > > cheers > Bruce > > > On Fri, 28 Apr 2017, Jared > Saletin wrote: > > > Hi Freesurfer Experts! > > > > I have two scans for each subject in a new experiment—taken on subsequent > > days, each using the MEMPRAGE protocol. > > > > I’ve successfully implemented DURA correction using the 4 echos when I’ve > > reconstructed each scan separately. > > > > However, since I have 2 scans for each subject, I was thinking rather than > > reconstruct the brain twice and average the thickness measurements, it > > would be better to feed both MEMPRAGE scans to recon-all. > > > > My question is if I do this, which echos should I use for Dura correction: > > day 1 or day 2 or is there a way to combine them into an average? > > > > Is this (feeding both days’ scans to recon-all) a reasonable strategy, or > > am I better to reconstruct the data separately? > > > > Thanks so much! > > Jared > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer at nmr.mgh.harvard.edu > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > > — Jared M. Saletin, PhD Assistant Professor of Psychiatry and Human Behavior Alpert Medical School of Brown University E.P. Bradley Sleep Research Lab 300 Duncan Drive Providence, RI 02906 Email: jared_sale...@brown.edu Phone: 401-421-9440 Fax: 401-453-3578
_______________________________________________ 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.
