External Email - Use Caution Hi Rosie,
I'm going to have to defer to others about questions on manual editing.. I've never done it! Sorry, -Paul On Thu, Jul 8, 2021 at 1:27 PM Rosalia Dacosta Aguayo <rdacos...@gmail.com> wrote: > External Email - Use Caution > > Hi Paul, > > Not sure what command I should run when I edit the brainmask because the > pial got too much. > > Kind regards, > Rosie > > > > > On Thu, Jul 8, 2021 at 6:13 PM Paul Wighton <p...@corticometrics.com> > wrote: > >> External Email - Use Caution >> >> Hi Rosie, >> >> >>> It is my first time editing wm segmentation (white matter segmentation >>> errors + topological errors). >>> >>> I wonder if there is a good tutorial on which I could rely. >>> >> >> There are a few tutorials that may be helpful (a full list of tutorials >> is here *MailScanner has detected a possible fraud attempt from >> "secure-web.cisco.com" claiming to be* >> https://secure-web.cisco.com/1czW6pKBcE24-CNRkxb6ooGpRPNjnMWsjYmV1Vm5VwXhF19Ayri9sGtlSRu6KwhloafCt-45d_tdPd7zrNSjI0joh8p04_0SjDgAN2KB7B1ws2LNAkXwAVBd0evPcrHZKY1mFIR1ta5anNbrhRrZYgOn35XIaxXYH8PFb62SrYTs1IqBsuXLyyG9nMqTHws0ZpELY9a8eg2EAIQmPBWpVa-_lBHVWrc_x2V4iNU3Dewf3oiYjo1BKr4zU20icECiH4oyoWt6itoTDT22RbIJDag/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FTutorials >> <https://secure-web.cisco.com/1rODvJs1ai8ocaVd_PRpeTFJnXk0wukmSM7yCNRCloKKL4ZPQZOCVExtqPxRRAOWBluRDRjQqno9QrifD6CT8o6C91nxLIK51ygwiD_a39suQIFvjfTIAwewDsrBzOPd0KafjQda5FJFwreS1HTt1HosPKu8vwfBtxK_-pjMFsWnozXAMp9NfzqiKFBVYdRwC2tKzjM4egHuUwi4z9lf6LD2g73pypGrmcJy2WLqaqKyrv8HZQznR_0PD-S2Yvn_wIR0dwiBFmkDXRxUl-Q8v_w/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FTutorials> >> ) >> >> - Introduction to Freesurfer Output (*MailScanner has detected a >> possible fraud attempt from "secure-web.cisco.com" claiming to be* >> https://secure-web.cisco.com/1Y4PmXm9jm0p3BdjnWrwYX4tVbC0r8t0gnjlMQI8M8MboDrdnDO44KZ7Iy-tVcPbD_KWBi2I21KzYc1bZdO9UZK6rBaXx9LWAQndjOM7AtGsQi3G10V9f9MAngt9BReLHHEkeocl63lwRLa0-63v14pHnlgmvzS1PyjJQ7LKr_9zhfT5JZZNXUdVhNvwUmBbsYuzntEms59g0D7k5HbbJ1_Hs8Rhrs3NvdphUYOSKxf97W1u1z6NVKpc63qyVrRtyNfBi8OZXiTFz2-kUe4qnAA/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsTutorial%2FOutputData_freeview >> <https://secure-web.cisco.com/18uPMHpt-EW_7l-sGIaivhnHa95jFiH6KEsNWb04DvYfYf5ZGlM1P6TunxF4ua8lyLPmgu4nvzTMwzZcdxgpYY5VayEiZvGZqVbJZ5D2JYEF5oTJxv7waaXt3YGX6jWknB4IjYDcr0omjY4c3L9yXXHLouBDOyWD-y-S2XtFdj5rSiS32CBQr9fuottLqbP1ApRZsrxO2C2BQY3-BldhPPwZuf5BG1Wk8kfubSeTdsQY5oHR0a_5P2pa15O22b_v8f96s2PK40XcUbmIyZJr2Pg/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsTutorial%2FOutputData_freeview> >> ) >> - Troubleshooting your output (*MailScanner has detected a possible >> fraud attempt from "secure-web.cisco.com" claiming to be* >> https://secure-web.cisco.com/17yG4rWY2JH-aueRtfCzJBhm5PI3rbAKiXFr2EQ9XFJf8sNeyMS0VLZxX_r6gQRO0UDl-R7GS87tdxeSsZ-oRPqZFoHoVA9tr_wqFLEZ8YFEhCufLp_cKnEt5uAiPMT_-Cr-T55QCX14awsJKny8f61U1VdU4pVvWNzsjMKUbo_bYxD1mgBn_N08oQ5FC8WgjewY54UjvXbzYccNK-lbHQCZT65ZywPwm6r7R_YMLJUG66rsezlsQuI8rZDcZRzJA7zJY9f_Khu9mS0OYOWzLJg/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsTutorial%2FTroubleshootingData >> <https://secure-web.cisco.com/1zI67HQZxy9cLn2I7uNmt2Vr-hMBP6KFcnjs-2A6egLkEI1MdK1Gq5cjgRVpOKFeY0BZHSQpCxQ_hvmo-1q_fm4W5LBFlzeRGLRkMeqnlLkCjVUHD91Mg4XY5bp69Vv4H6Ki2R5vSBBt-vqF1FTgrVYSdUrw2DT9R9zxt4y9rWxSh5-0__pOG9knY3Wo_iwk1tqsMMeTL6-stQkgJwC6RUi7qglYapWN7yyR5yIfYachGm9H6TULtIlGONzwBDlLjpFHrzKvuV3VeugenXt3RuA/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsTutorial%2FTroubleshootingData> >> ) >> - Quality Check a FreeSurfer Recon Demo (*MailScanner has detected a >> possible fraud attempt from "secure-web.cisco.com" claiming to be* >> https://secure-web.cisco.com/1nlexAM5p5xH0PFNwe-wszdujC8ps20WrOdXBNj2DUuBJiESaJrRR_KNJc0Dpli-dtfX9C1DoHBmrX5ZXwnhp9ThEXgOHdGlpqlftOZe_GFRdQKmiUlh3dDtfADLmGmzwT6RiH8sEp4NMPCqZ6Ab75GZ33DSsIyg_Nb7vfHNpAjn44Ym27FMr4pktLATBkdquGqAO9eBXCu1Fij_30cWgAPHZj_qSVTN_6UUVIPXLoBQTNQOcAYaR-EAJRqfPPEIJRWUrEzUTtoJRy2_2KedhuA/https%3A%2F%2Fwww.youtube.com%2Fwatch%3Fv%3DAR83_Bt04VQ >> <https://secure-web.cisco.com/1QerwbflgUAsGFSC22lK8ez-lDsA9D3P7CJypkBpY72fGywKINhle2vo9kPS3sRJshRi7RBTgT3m5i4YzA51pzGB9J7ozBiNK_3EJYqP80jsPsR2MgunkxzNuzhwrWyjyAkDaKuii2Ak2stl5dJifUtwrZ80fr8twb486IsKisN8ktU2NQ-NBSzVzwIcltDwaBTYGPzQrKb2zwAXiXm-V3z4TdghHvMclkYac6iKI1Y70xc6GPHROPaVuBFPqBIGI4chLrGmPOYRQ_r6QDW9VtA/https%3A%2F%2Fwww.youtube.com%2Fwatch%3Fv%3DAR83_Bt04VQ> >> ) >> >> Also, I have read there is an example of segmentation that comes with >>> FreeSurfer that is called Bert. I think it would be great to have it so I >>> can look at it as a good example. >>> >> >> There should be an example that comes with the FreeSurfer installation. >> I can't remember exactly what comes with v6, but you should find more info >> with `cat $FREESURFER_HOME/subjects/README` >> >> Good luck! >> >> -Paul >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> *MailScanner has detected a possible fraud attempt from >> "secure-web.cisco.com" claiming to be* >> https://secure-web.cisco.com/112Glt1gX_olau1BV9wt47Kjp-lYXwPtZPmaB7dVahHaKCPMnxOpUrDbVbzf2a6Dn4WK4vloOKllQCNW-XT7CW8jMVFuzVudwZBw50l9XXUKhE9B7tddSDbNdgdHWjCZrcsunYeF6SE7QF18c8K8WG6EFjr7NXjv5f-CFEJWE7PbvDm04fQ3eq9u0djuT4wgZN18NYFczTtk4tR5jGRGrkrfo2Uu_4P9lvtQ7XoumHUPpmpt7Mm5vW6yC9YwhqRxgfqRcHaIJaIyuFbR-x1lr3A/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer >> <https://secure-web.cisco.com/1DHbxGoPwPUUJCixsnh0mQrCQIauHUV98bwCgaNLKb83X09xBfK7o3X7Uj5F1Y6vzxIjPlgV3ZT2vp7aXbVPuSqFUlzb0B7FLzyGgqeZqPmkAJjw3lKAfF7RIsCffMVJ9jCBMQA-Vgekre5xLOi3QnMERQYAK1OVgBr2yQOkgGEPmchh-WHSaNpec76HTrPZ0oPHAfDDUZzQuwMJ7eLtNnMV9QlgJrwqumWlesuSvss-zlM0815iNPvDqSGyL7Og3ArkzucOeLoxq2I9Zkh3aAQ/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer> > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://secure-web.cisco.com/112Glt1gX_olau1BV9wt47Kjp-lYXwPtZPmaB7dVahHaKCPMnxOpUrDbVbzf2a6Dn4WK4vloOKllQCNW-XT7CW8jMVFuzVudwZBw50l9XXUKhE9B7tddSDbNdgdHWjCZrcsunYeF6SE7QF18c8K8WG6EFjr7NXjv5f-CFEJWE7PbvDm04fQ3eq9u0djuT4wgZN18NYFczTtk4tR5jGRGrkrfo2Uu_4P9lvtQ7XoumHUPpmpt7Mm5vW6yC9YwhqRxgfqRcHaIJaIyuFbR-x1lr3A/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
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