Re: [Freesurfer] SAMSEG longitudinal sbTIV bigger than - Freesurfer

27 Sep 2022

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Thank you for the response.
I've attached the log files for each cross sectional analysis separately and the longitudinal as one log file.
Cross-sectional commandline:
run_samseg -I sub-001_tp1_T1.nii.gz --threads 4  -o result_sub-001
longitudinal commandline:
mri_robust_template --mov sub-001_tp1_T1.nii.gz sub-001_tp2_T1.nii.gz sub-001_tp3_T1.nii.gz --template mean_sub-001.mgz --satit --mapmov sub-001_tp0_T1.mgz sub-001_tp1_T1.mgz sub-001_tp2_T1.mgz
run_samseg_long --timepoint sub-001_tp0_T1.mgz --timepoint sub-001_tp1_T1.mgz --timepoint sub-001_tp2_T1.mgz --threads 4 -o result_sub-001_long
I believe this was the command line suggested by https://secure-web.cisco.com/1oqDIm79n7D7QLNKEDd942zigkcTJZXoH4tRx3rNojVf-E-...
Thank you,
David
Message: 3
Date: Mon, 26 Sep 2022 22:14:37 -0400
From: "Douglas N. Greve" dgreve@mgh.harvard.edu
Subject: Re: [Freesurfer] SAMSEG longitudinal sbTIV bigger than
    cross-sectional
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: 34a07418-b022-160b-bfac-39c493226f28@mgh.harvard.edu
Content-Type: text/plain; charset="utf-8"
Can you send your command line and log file? In particular, how did you 
register the time points?
On 9/26/2022 6:46 AM, Nederpelt, D.R. van (David) wrote:
...
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Dear SAMSEG developers,
We have a dataset with 55 subjects (MS patients and controls) scanned 
on three timepoints with yearly intervals.
When we ran the (SAMSEG) longitudinal pipeline we noticed that the 
sbTIV always had an increased volume (between 0.5 and 3.5% larger) 
compared to the sbTIV computed cross-sectionally. Do you have any idea 
how and why we may see these effects?
Thank you in advance!
Best regards,
David van Nederpelt | Amsterdam UMC

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