Re: [Freesurfer] Using multiple MEMPRAGE scans as input to recon-all: which echos to use for dura correction?
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_saletin@brown.edu Phone: 401-421-9440 Fax: 401-453-3578
Hi Jared
again it depends on data quality. If it is good enough you are probably better off just picking the best scan and reconning it.
cheers Bruce
On Mon, 1 May 2017, Jared Saletin wrote:
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 woul d 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
—
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_saletin@brown.edu Phone: 401-421-9440 Fax: 401-453-3578
freesurfer@nmr.mgh.harvard.edu
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Bruce Fischl -
Jared Saletin