Hello Agata,

From my limited knowledge, it is not possible to update the segmentations and re-run the recons at this point.

Karthik

On Apr 5, 2024, at 10:31 AM, Agata Wolna awolna@mit.edu wrote:

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Hi!

I have a question regarding the recon-all-clinical pipeline: is it possible to edit the outputs of the synthseg segmentation run as a part of the pipeline (synthseg.mgz) similarly to editing recons from the standard freesurfer pipeline, and getting updated segmentation estimates (the synthseg.vol.csv files) for these manually updated segmentation?

Thanks for your help! Agata _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer