Hi Jee Won,

Currently the infant stream does not allow for a rerun after manual edits. Editing the thalamus though would not impact the surface computations though.

Best, Lilla ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Kang, Jee Won JeeWon.Kang@childrens.harvard.edu Sent: Thursday, February 16, 2023 8:38 AM To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Infant Freesurfer - manual edits

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Dear Freesurfer experts,

Hello, I have started experimenting with Infant Freesurfer (version 4a14499), and we have run into a problem with very poor segmentation of the thalamus in one of our subjects.

Is there a way to incorporate manual edits, as in adult Freesurfer, to improve the segmentation? From this post: MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg65925.htmlhttps://secure-web.cisco.com/1A3X8CGDC9HIB1-7GzN2d3Jhl_jxtbWw34-Ck5nrUNk5fVAdyLCWHjN5ap2azPBqPsSc3sy6BDPgWQ8_o95xSmPjZyTJ12y62Dmj4XaI1Nn-8gKibNYWKcV_DDuhG3kA5N3kt5sbXihGLqugecs4PiV9Y7Cre0gljwzIcvqcS5bwIKeVXbNsel4OeFR8IavTMlxXf_oQSzI0OkbTJ1bDFhT0xS2IbjGMihkFMaVo5uYKbGpWbONFzi22uaAgX0oaE21gYcZiq0iiBQ9GXTbuXT-h9gCAabJNWTxzU5NuB3Qc0wqQodr2LVedoh_-igNPu_Q4TymJr1J7epwMSqyrS1A/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg65925.html, it looks like the option to make manual edits was a feature in the works, but I am not sure if that is still the case.

I am guessing it would be inadvisable to re-run the infant data after making edits (to wm or aseg.presurf) in adult Freesurfer?

Thank you for your advice on this!

Sincerely,

Jee Won