Apologies! I don’t believe you can run the recon-all-clinical approach for longitudinal work, as many of our intermediate files (e.g., norm.mgz) are not directly comparable to the ones in the standard recon-all stream as of now. 

Karthik

On Nov 26, 2024, at 9:03 AM, 王又劼 <wangyoujie2002@163.com> wrote:

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Hello,

I have longitudinal imaging data for some participants. Due to the data collection protocol, the T1w image from the first timepoint (TP1) is a clinical sequence (e.g., slice thickness of 5mm or 6.5mm), while subsequent timepoints collected 3D T1w images with a slice thickness of 1mm. My study focuses on analyzing cortical thickness changes in participants over time. I have the following questions:

  1. I plan to use recon-all-clinical to analyze the clinical T1w data. However, I noticed that the official documentation mentions that slice thickness significantly impacts cortical thickness estimation. Are there any acceptable methods for comparing cortical thickness changes across different timepoints for the same participants?
  2. Can the results of recon-all-clinical be used in FreeSurfer's longitudinal workflow?

I have searched archived mails and reviewed studies citing articles related to recon-all-clinical but have not found relevant answers. I would greatly appreciate any help on this matter.

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