Dear Nima, As of today, there is no longitudinal version of recon-all-clinical. It’s a bit tricky to adapt the standard longitudinal pipeline in FreeSurfer to scans with thick slices due to the anisotropy of the images, and also due to the deep learning bits of the pipeline. But you can of course use the cross sectional measurements in your longitudinal study. Kind regards, Eugenio
-- Juan Eugenio Iglesias http://www.jeiglesias.com From: freesurfer-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Taghizadeh Mortezaei, Nima <ntaghizadehmortez...@mgh.harvard.edu> Date: Tuesday, February 11, 2025 at 11:34 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Inquiry About Longitudinal Analysis Using recon-all-clinical.sh I appreciate any guidance or recommendations for my question. ________________________________ From: Taghizadeh Mortezaei, Nima Sent: Tuesday, February 11, 2025 9:45:25 AM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> Subject: Inquiry About Longitudinal Analysis Using recon-all-clinical.sh Dear FreeSurfer Community, I want to work on a longitudinal analysis with two time points (pre-treatment and post-treatment) and would like to follow the recommended longitudinal pipeline. However, I want to use recon-all-clinical.sh and I want to ask whether the commands and steps for recon-all-clinical.sh are the same as the standard recon-all longitudinal pipeline? Are there any modifications or additional considerations required when using this script for longitudinal processing? I appreciate any guidance or documentation references that could help with this analysis. Thank you for your time and support! Nima
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