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Hi Kersten,

Thank you for your response. Am I able to do ROI analysis (following whole-brain analysis) using the mris_preproc and mris_surf2surf outputs (which I am currently using for whole-brain analysis)? I was under the impression that aparcstats2table output is simplest for ROI parcellation, so I used that to prep the data.

Best, Daniel From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Diers, Kersten /DZNE Sent: January 7, 2025 8:51 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Fwd: LME pipeline for individual ROIs

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External Email - Use Caution Hello,

I am not sure if there is a right or wrong here; personally, I'd do a single whole-brain analysis, and apply ROIs only as the very last step, correcting for multiple comparisons within each ROI and for the number of ROIs. I would not expect fundamental differences between this approach and your approach, though.

FDR2 may be more sensitive than FDR, but not necessarily in all circumstances.

Hope this helps,

Kersten

External Email - Use Caution Hello FreeSurfer experts,

I am using a mass-univariate pipeline to assess cortical thickness changes longitudinally at a regional level (based on the D-K atlas), and have been following this thread: MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to behttps://http://secure-web.cisco.com/1Ek1ZeG4YDYXBH43CB4cilld8YgBEeoTTjAOOv39...https://secure-web.cisco.com/1gfQ9eWAEqDZ3DGmI9NL7F2WPKbHBLsM60VyuP_LVR3dT1CV3DkQLnS7V3mw52P2LBaCekNfBwRZ37ft6dOBwXhzUo_wrbKJVG2XMB6GHfBDDPgLMXLkX7heqJ_KkmWwqJy9piolbuNnl5eaQ39pcYUHcoICiPTjHmCz39Kf6z2NQq9upBO5S0R7ruzTcfdlTWq2KiXcwnU5TGmYC3srVmnpf9O6iRWBD-KwL6sYWR9N7oVhfzBX4MGtQvWaZLqWHR1O2oClgbUhcdWbD_-CG15C0wAv3HIAwKDxQQ4Xz1z8IN_wUzZ3LBykDu0uR2LrPr465UModBjZSGhvR14zGWw/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg76987.html.

My pipeline is set up so that lme_mass_fit, lme_mass_F, and lme_mass_FDR are all run independently in a for-loop for each individual ROI, rather than altogether. Is this correct? As well, would using FDR2 be more advantageous than FDR?

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