External Email - Use Caution
Dear Falk,
I tried to search your poster presentation in the 2018 ISMRM web but unfortunately I did not find it. Can you attach the link? I would be interested in this information and how to proceed.
Thanks in advance,
Best,
El vie., 12 oct. 2018 a las 13:59, Falk Lüsebrink (falk.luesebrink@ovgu.de) escribió:
External Email - Use CautionDear Lisa,
what you potentially can do is to use the denoised surface (*h.white) as a starting point (instead of *h.orig) in the unfiltered stream. This should remove any bias introduced by the denoising, however, you should gain the advantages of denoised surfaces, e.g. less need for manual intervention, less topological defects, etc.
I had a poster presentation for this method at last ISMRM.
Best,
Falk
*Von:* freesurfer-bounces@nmr.mgh.harvard.edu [mailto: freesurfer-bounces@nmr.mgh.harvard.edu] *Im Auftrag von *Lisa Crystal Krishnamurthy *Gesendet:* Donnerstag, 11. Oktober 2018 19:07 *An:* Freesurfer support list freesurfer@nmr.mgh.harvard.edu *Betreff:* Re: [Freesurfer] denoising and recon-all {Disarmed}
External Email - Use Caution *The ONLM denoising algorithm in the following package: (*MailScanner has detected a possible fraud attempt from "na01.safelinks.protection.outlook.com" claiming to be* https://sites.google.com/site/pierrickcoupe/softwares/denoising-for-medical-... https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fsites.google.com%2Fsite%2Fpierrickcoupe%2Fsoftwares%2Fdenoising-for-medical-imaging&data=02%7C01%7Clkrishnamurthy%40gsu.edu%7Cadf6338b011843f3549d08d62f89e5d0%7C515ad73d8d5e4169895c9789dc742a70%7C0%7C0%7C636748666676225518&sdata=F0mfd%2B63mdYPHplRq4jcjz9FuSvE2nUxMxqDlFfIZB4%3D&reserved=0 )
Best,
-Lisa
*From:* freesurfer-bounces@nmr.mgh.harvard.edu [ mailto:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu] *On Behalf Of *Glasser, Matthew *Sent:* Thursday, October 11, 2018 12:39 PM *To:* Freesurfer support list *Subject:* Re: [Freesurfer] denoising and recon-all
External Email - Use Caution *What are you using for denoising?
Matt.
*From: *freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Lisa Crystal Krishnamurthy lkrishnamurthy@gsu.edu *Reply-To: *Freesurfer support list freesurfer@nmr.mgh.harvard.edu *Date: *Thursday, October 11, 2018 at 11:05 AM *To: *"freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu *Subject: *[Freesurfer] denoising and recon-all
External Email - Use Caution *Hi,
I have found that denoising the MPRAGE prior to FS recon-all seems to improve the segmentation (see attached pdf). However, it is not clear if the denoising algorithm may cause some signal intensity changes (especially in voxels with partial voluming at the edge of the brain) that violate assumptions of recon-all. Could you help me understand what the assumptions of your algorithm are, and what I need to do to make sure my images conform to those assumptions?
Your help is greatly appreciated.
Best,
-Lisa
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