Subject:	Re: [Freesurfer] SAMSEG longitudinal processing questions
Date:	Thu, 28 Jan 2021 16:45:39 +0000
From:	Stefano Cerri <stce@dtu.dk>
To:	Douglas N. Greve <dgreve@mgh.harvard.edu>
CC:	Koen Van Leemput <leempko@gmail.com>

1) SAMSEG long should compute more consistent longitudinal structural volumes than SAMSEG while detecting better volumetric group differences (cf. Table 1 and Fig 3 of https://arxiv.org/pdf/2008.05117.pdf). Yes, using SBTIV for correcting volume changes from different scanners would be beneficial and most probably necessary.

2) The lesion version of SAMSEG long is available in the development version. Enabling the lesion extension can be done by adding the same flag(s) as for the cross-sectional lesion version (--lesion, see the Wiki for details: https://surfer.nmr.mgh.harvard.edu/fswiki/Samseg)

3) We never conducted extensive experiments for the number of burn-in and samples for the MCMC scheme, but we found that 50 burn-in and 50 samples lead to robust and replicable lesion segmentation results. Increasing these two numbers might increase the lesion segmentation performance, although differences might be minimal and the overall computational cost high. We suggest to not decrease these two numbers as lesion performance could potentially decrease.

Best,

Stefano

From: Douglas N. Greve <dgreve@mgh.harvard.edu>
Sent: 28 January 2021 16:30
To: Koen Van Leemput; Stefano Cerri
Subject: Fwd: [Freesurfer] SAMSEG longitudinal processing questions

-------- Forwarded Message --------

Subject:	[Freesurfer] SAMSEG longitudinal processing questions
Date:	Thu, 28 Jan 2021 09:37:32 -0500
From:	XY XY <kamsonmd@gmail.com>
Reply-To:	Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
To:	freesurfer@nmr.mgh.harvard.edu

External Email - Use Caution
Hi FreeSurfers,

Thank you for sharing the new SAMSEG tool, which I consider a major breakthrough in image processing!
I have a few questions about using SAMSEG vs SAMSEG_Long:

1. What volumetric differences should I expect between running SAMSEG on individual images, vs. using SAMSEG_Long for the longitudinal analysis? Could I use SBTIV to adjust differences between scans?
(all images are FLAIRs preprocessed using mrI_robust_template)

2. Is there currently a way to integrate lesion segmentation into the SAMSEG_long’s longitudinal analysis?

3. What is the expected impact of increasing or decreasing -Burn-In and -Sample numbers for lesion segmentation?

Thank you for all the help!

Best,

Dave Kamson

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