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@tsalo tsalo commented Oct 17, 2025

Closes #3507. As of 25.1.0, tedana has an --exclude parameter in its t2smap CLI, which allows users to ignore certain volumes when estimating T2* and S0. This PR bumps the tedana version and leverages that parameter to ignore dummy scans. If it proves useful, we could also ignore high-motion volumes in the future.

Changes proposed in this pull request

  • Increase minimum tedana version from 25.0.0 to 25.1.0.
  • Use estimated number of dummy scans to set exclude parameter in t2smap call, so that those volumes do not contribute to the estimation of T2*, which is in turn used to optimally combine the data across echoes. I doubt the dummy scans actually have much effect on T2* estimation, but it still stands to reason that they are not helping.

Documentation that should be reviewed

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tsalo commented Oct 17, 2025

I tried running pixi lock to update the lockfile, but it doesn't seem to work on my Mac.

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T2* estimation appears to use dummy volumes

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