I don't think you have this set up properly for the RM ANOVA. You'd have to have a different class for each input. It looks like you've partially configured for the paired analysis https://surfer.nmr.mgh.harvard.edu/fswiki/PairedAnalysis, which is probably the easier thing to do, but somthing looks wrong in your FSGD file. If using the paired analysis, then you should have subtracted time point 1 from 2 (or the other way around), so you have one map per subject (not two, as in the RM ANOVA), and so one line for each subject in the FSGD. If you have two classes (Lang and Control), then you are in the Two Group, Zero covariates situation here https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf2G0V

On 4/14/2025 8:32 AM, Emilia Rydén wrote:

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Hi everyone,

I’m new to FreeSurfer and currently working on a group-by-time analysis. I have two groups (language and control) and two time points (pre and post). I’m planning to run a repeated measures ANOVA using the approach described here: *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://surfer.nmr.mgh.harvard.edu/fswiki/RepeatedMeasuresAnova https://secure-web.cisco.com/17-MXDv-625h05yLHVA36RwisjCP6uV-tVc6FhAka3PqeNpIrJVhokxzKjHAkGt0Dl7h45H6c5dgt-nPARKPDSKbu4k_6Gm2KGe9q1BTKjDfVEHmhLTKcb8SFw7Y-oZpu0xBzGyEmIMGYLmPoHbPOZQa5xBaRNpOMVLIX0m0pm5hJZuxJH5AxorOVpLmFhNqCasfmlr5MW0KcOwxqOCPHjicK0XM-HVRD5c5R_MtCD1vB-8FzydEtCIrToCXLY5iz-vCAG9E2VQeV471UlYp4jVn6na7hhEOqh_sOdjl8HW4E-CL6W1T-DexPBp9SVdGfo_gp_oGBAZvwVUorV1WJMw/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FRepeatedMeasuresAnova.

I’ve attached my initial attempt at an FSDG file. I would greatly appreciate any guidance on how to correctly model this, particularly when it comes to setting up the contrast files.

Thank you in advance for your help!

Best regards, Emilia

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