External Email - Use Caution
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:
????????External Email - Use Caution
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
VUmc disclaimer : http://secure-web.cisco.com/1EbjEQdohUHHbwqoXgtELvuZtoJbA4FpYVDb696sqA2OCCMK... AMC disclaimer : http://secure-web.cisco.com/1OKBQzdi-SpM4JCdLoqAd96KeYXkbEWuzJHlDAdSqXAevsHr...
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1BSAqf9q22bDxY2klFhioiJ1vAOoopvo6KQDUssTUdioRpD...