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Union of all TN modifications

Tom Nichols requested to merge nichols/ukb_unconfound_v2:AllTNmods into master

I have tried to fastideously create a series of seperate MRs (merge requests) that isolate different changes. In the end, however, you may not want to bother with each individual set of changes. This MR encompasses all of the other MRs as follows:

  • !1 Amend wrapper_funpack
  • !2 Fix generate_initial_data/README.md formatting
  • !3 Fix wrapper_funpack.sh
  • !4 Update generate_initial_data/README.md (bash_scripts)
  • !5 Add files to bash_scripts
  • !6 Add absolute paths for FSL commands
  • !7 Various changes
  • !9 Fix call of script_FLIPPEDSWI_serial.sh from script_initial_workspace.sh

To be clear... this MR supercedes all the above MRs... if this MR is merged, the above MRs can be closed.

Edited by Tom Nichols

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