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@satra Topofit uses freesurfer for preprocessing the inputs before inference. Should we include freesurfer as a requirement to enable preprocessing or should we warn the user that the data has to be preprocessed first outside the zoo?
you can make preprocess an option. presumably you can use the minimal freesurfer for this instead of all of freesurfer. see neurodocker for the min recon-all version. however this can be one of those MVP, MVP+1 things. MVP - don't include, file an issue, include in MVP + 1.
The saved model and predict.py scripts can be found at https://github.com/neuroneural/topofit_fork.
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