Forwarding Stefano's answers...
-------- Forwarded Message --------
Subject: Re: [Freesurfer] SAMSEG longitudinal processing questions
Date: Thu, 28 Jan 2021 16:45:39 +0000
From: Stefano Cerri <s...@dtu.dk>
To: Douglas N. Greve <dgr...@mgh.harvard.edu>
CC: Koen Van Leemput <leem...@gmail.com>
External Email - Use Caution
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 <dgr...@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 <kamso...@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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