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Hi! I was wondering whether the issues with surface reconstruction from MP2RAGE data that were reported for Freesurfer v5.1 in Fujimoto et al., 2014 still persist in more recent releases of Freesurfer, and whether there is information to what extent they apply to 3T data? Thank you! Caspar
Hi Caspar
Can you elaborate? What are the issues? Bruce
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Caspar M. Schwiedrzik Sent: Monday, September 7, 2020 2:27 AM To: Freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] MEMPRAGE vs. MP2RAGE
External Email - Use Caution Hi! I was wondering whether the issues with surface reconstruction from MP2RAGE data that were reported for Freesurfer v5.1 in Fujimoto et al., 2014 still persist in more recent releases of Freesurfer, and whether there is information to what extent they apply to 3T data? Thank you! Caspar
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Hi Bruce, In that paper, you reported that MP2RAGE underestimates cortical thickness relative to MEMPRAGE and also has slightly lower reproducibility. Since Recon-all does not seem to have built in functionality to deal with the background noise in MP2RAGE, I am wondering whether you still recommend MEMPRAGE over MP2RAGE. I only have regular MPRAGE for comparison at the moment. Thank you, Caspar
On Mon, Sep 7, 2020 at 19:56 Fischl, Bruce BFISCHL@mgh.harvard.edu wrote:
Hi Caspar
Can you elaborate? What are the issues?
Bruce
*From:* freesurfer-bounces@nmr.mgh.harvard.edu < freesurfer-bounces@nmr.mgh.harvard.edu>
*On Behalf Of *Caspar M. Schwiedrzik
*Sent:* Monday, September 7, 2020 2:27 AM
*To:* Freesurfer@nmr.mgh.harvard.edu
*Subject:* [Freesurfer] MEMPRAGE vs. MP2RAGE
External Email - Use Caution *Hi!
I was wondering whether the issues with surface reconstruction from MP2RAGE data that were reported for Freesurfer v5.1 in Fujimoto et al., 2014 still persist in more recent releases of Freesurfer, and whether there is information to what
extent they apply to 3T data?
Thank you!
Caspar
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https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.ed...
Oh, sorry, yes I remember now. I guess mp2rage naturally sacrifices some SNR/unit time to get flatter images. I think Doug (and Jon, now included) can comment on this
Cheers Bruce
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Caspar M. Schwiedrzik Sent: Monday, September 7, 2020 2:26 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] MEMPRAGE vs. MP2RAGE
External Email - Use Caution Hi Bruce, In that paper, you reported that MP2RAGE underestimates cortical thickness relative to MEMPRAGE and also has slightly lower reproducibility. Since Recon-all does not seem to have built in functionality to deal with the background noise in MP2RAGE, I am wondering whether you still recommend MEMPRAGE over MP2RAGE. I only have regular MPRAGE for comparison at the moment. Thank you, Caspar
On Mon, Sep 7, 2020 at 19:56 Fischl, Bruce <BFISCHL@mgh.harvard.edumailto:BFISCHL@mgh.harvard.edu> wrote:
Hi Caspar
Can you elaborate? What are the issues?
Bruce
From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu>
On Behalf Of Caspar M. Schwiedrzik
Sent: Monday, September 7, 2020 2:27 AM
To: Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] MEMPRAGE vs. MP2RAGE
External Email - Use Caution
Hi!
I was wondering whether the issues with surface reconstruction from MP2RAGE data that were reported for Freesurfer v5.1 in Fujimoto et al., 2014 still persist in more recent releases of Freesurfer, and whether there is information to what
extent they apply to 3T data?
Thank you!
Caspar
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Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu
https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.ed...
The noise properties depends on the sequence, but the MP2RAGE sequence I use is a little noisier than the MEMPRAGE. The B0 distortion is different. Since it is a different sequence, there will be systematic differences between the acqs. Generally, this is nothing to be done about it. The bias will probably affect all groups the same, so it will not affect your final group stats much.
On 9/7/2020 3:09 PM, Fischl, Bruce wrote:
Oh, sorry, yes I remember now. I guess mp2rage naturally sacrifices some SNR/unit time to get flatter images. I think Doug (and Jon, now included) can comment on this
Cheers
Bruce
*From:* freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu *On Behalf Of *Caspar M. Schwiedrzik *Sent:* Monday, September 7, 2020 2:26 PM *To:* Freesurfer support list freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] MEMPRAGE vs. MP2RAGE
* External Email - Use Caution *
Hi Bruce,
In that paper, you reported that MP2RAGE underestimates cortical thickness relative to MEMPRAGE and also has slightly lower reproducibility.
Since Recon-all does not seem to have built in functionality to deal with the background noise in MP2RAGE, I am wondering whether you still recommend MEMPRAGE over MP2RAGE. I only have regular MPRAGE for comparison at the moment. Thank you,
Caspar
On Mon, Sep 7, 2020 at 19:56 Fischl, Bruce <BFISCHL@mgh.harvard.edu mailto:BFISCHL@mgh.harvard.edu> wrote:
Hi Caspar Can you elaborate? What are the issues? Bruce *From:* freesurfer-bounces@nmr.mgh.harvard.edu <mailto:freesurfer-bounces@nmr.mgh.harvard.edu> <freesurfer-bounces@nmr.mgh.harvard.edu <mailto:freesurfer-bounces@nmr.mgh.harvard.edu>> *On Behalf Of *Caspar M. Schwiedrzik *Sent:* Monday, September 7, 2020 2:27 AM *To:* Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> *Subject:* [Freesurfer] MEMPRAGE vs. MP2RAGE * External Email - Use Caution * Hi! I was wondering whether the issues with surface reconstruction from MP2RAGE data that were reported for Freesurfer v5.1 in Fujimoto et al., 2014 still persist in more recent releases of Freesurfer, and whether there is information to what extent they apply to 3T data? Thank you! Caspar _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.edu_mailman_listinfo_freesurfer&d=DwICAg&c=JeTkUgVztGMmhKYjxsy2rfoWYibK1YmxXez1G3oNStg&r=sgvCAzCi3iTXkTNRRVMpDnC6tu0lnijYpKXIX_UNme8&m=xQ8Cowc6OmPjU8ym3EVysBmtoEVDE6H47AkCObdzVy8&s=cUIYIUPYlPPYzq9yUoARG1sjLpuraBvjMrsd31fx1g8&e=
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Fischl, Bruce