External Email - Use Caution Yes, it looks fine to me Those dots seem to lie on the pial surface
On Thu, Mar 7, 2024, 10:07 PM Douglas N. Greve <dgr...@mgh.harvard.edu> wrote: > Have you looked at the actual surface? > > On 3/7/2024 2:29 AM, Hyunchul Lee wrote: > > External Email - Use Caution > Hello, > I'm using Freesurfer recon-all to create reconstructions to use with > MNE-python for source estimation of SEEG data. My work relies on having > correct labeling of segmentation data. For most cases, there has been no > trouble but I am having trouble where the cortical parcellation shows up as > dots in one hemisphere. Please see image attached. I also noticed that the > lh.ribbon.mgz is also 'dotty' (also attached). There is no issue with the > right hemisphere. This reconstruction was not manually edited, but only > recon-all was used. > > I have tried using mris_volmask --label_left_ribbon, setting the argument > to various values. That didn't work that great - reducing to 0 basically > whites everything out except for the white matter on the ipsilateral > hemisphere and anything 1 or more produces the same 'dots'. Interestingly > the pial and wm surfaces all look ok. Also, I am not sure if creating the > correct ribbon.mgz is going to fix the aparc.a2009+aseg file. > > I would really appreciate your advice. > > Best regards, > > *Hyunchul Lee* MBBS PhD > > _______________________________________________ > Freesurfer mailing > listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://secure-web.cisco.com/1_qngHgnIXXaLUJMegUyNQvKr4XQPNHtebLlFqn1mcfYS3tsajrOEk6JgszQ1fc2R6qFdNqMnpqG09V7I7C7IleMg4jcU1TW8tEivMyrhpMjvIdCTVE3pGppbi3uu3FkvkNMWCfHwcPE9wnwBiTgyqqxsB-YZr1d5-3KSZ8UgFWw7u14Yzx_0tCRQz--exUr-Ym0c4EoVRWFvR24M0vFAkIylKdpyHcUFeEumShGXcW6ql1ZVJsJFWfE_oMQB08PUr1GE-RDFy6v_-zSjGrwq451DFeGVfA85BsU8du-uZ2_VceE7w5TdKX4chAunIRUZOSxb2-4UXan0WHX24EO83w/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer > 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://secure-web.cisco.com/17tXD8icr3R6VE3cwvDvlr4diep7UgIV_i8fbM-ukTaC8tXXT29Z6rUX1vZnqZdNjz3U7YpY_kCfrkME-9qPo6hMEJRQAc-XKm971UHk0lnNI55KfCuoBNogH1Tp3otWKpadmmJWx87oII0QfbWoPsboE5gjyTXNcqnZdo5QRc3I9OoJuR5bHXezJVmpxL19gM1FPFOkXKpZUo5PrldgO-wuEXVSxeS0LT7_Zpnu4R0wb7NgIqiTVZcOPkMiS0hpdnMqoz1dJyph6lMnvvOFMWlxD4QzANaQW62fZS0Dszr9J5ctMT0DlYhfrplWKrOyc6pgYqyXPr0-i_CKmsyAG4A/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline > < > https://secure-web.cisco.com/17tXD8icr3R6VE3cwvDvlr4diep7UgIV_i8fbM-ukTaC8tXXT29Z6rUX1vZnqZdNjz3U7YpY_kCfrkME-9qPo6hMEJRQAc-XKm971UHk0lnNI55KfCuoBNogH1Tp3otWKpadmmJWx87oII0QfbWoPsboE5gjyTXNcqnZdo5QRc3I9OoJuR5bHXezJVmpxL19gM1FPFOkXKpZUo5PrldgO-wuEXVSxeS0LT7_Zpnu4R0wb7NgIqiTVZcOPkMiS0hpdnMqoz1dJyph6lMnvvOFMWlxD4QzANaQW62fZS0Dszr9J5ctMT0DlYhfrplWKrOyc6pgYqyXPr0-i_CKmsyAG4A/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline> > . >
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