Hi Dan, I have not worked with this code in a decade, but Kersten in my group maintains our R package of it ( see https://github.com/deep-mi/fslmer ). I will bring this to his attention.
Basically I think you determine the joint p-threshold across hemispheres and convert it to FreeSurfer ( - log10 pth) and use that value as a threshold when plotting the original p-values. That way you only need one threshold for the full plot, rather than two different ones (or the more pessimistic of the two). Also you may be interested in our whippersnappy python tool to generate nice looking screenshots of the surface overlay: https://github.com/Deep-MI/whippersnappy which is pip installable. Best, Martin On 2. May 2024, at 20:25, Dan Levitas <djlevitas...@gmail.com> wrote: Hi Martin, Thanks for the response! After my original post I went through things more carefully based on my two original two questions and made a follow-up post here (https://secure-web.cisco.com/1sMx-dupqFSyAsxsQl8ukXwR4v0-vTUkX2pc5vfwlqp166rCrDoo2bdx6p4keFMRMtTwBjqZmzCoopCuxETJGlS8kVcVUlFiUtWqouZifh-kkm5McZTXjC343IuxhPxggRZIGBfOCndTyBEfHU5yg-L0SF7Jk48ZP-_Yqg9JiZoQkXi347bobVlhhfUqU5umz6cI2eBD7bplC11HyJwUubhLdjnAYGV4QPy_JoqteaGamkmGiiirkesm6JsOmE4dUgh5w8JJfJIwHhiSus176NtxI70y9Cnc5-fIyFxbJ4NUpR41z8diD-6jjtGRt3yoMyyevPtGsNu9rgHK_-JalrQ/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg76783.html) with two final questions. The gist of these is that I’m unsure how to apply my multiple comparisons (for both hemispheres) to the analysis and subsequent visualization. Do you have any guidance on how I should proceed. Much appreciated, Dan
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline <https://www.massgeneralbrigham.org/complianceline> . Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.
